diff --git a/repo_utils/answer_key/bench/bench_bnd/candidate.refine.bed b/repo_utils/answer_key/bench/bench_bnd/candidate.refine.bed index c5259f82..a17ec96f 100644 --- a/repo_utils/answer_key/bench/bench_bnd/candidate.refine.bed +++ b/repo_utils/answer_key/bench/bench_bnd/candidate.refine.bed @@ -1,24 +1,37 @@ chr1 181135 181156 chr1 6005049 6006670 +chr1 122627325 122627346 chr1 224013761 224013782 chr10 1238267 1238288 chr10 39478703 39478724 +chr10 67470500 67470521 +chr10 68211488 68211509 chr10 132505641 132506422 chr11 964817 964838 +chr11 33648565 33648586 chr11 44662925 44662946 chr11 48880455 48880476 chr11 48888289 48888310 -chr11 68232223 68232244 +chr11 68232220 68233087 chr11 80583401 80583422 -chr11 105902622 105902643 +chr11 105902622 105902647 +chr11 125661462 125661483 +chr11 135076371 135076392 chr12 2572354 2572375 chr12 10428997 10444441 +chr12 24759747 24759768 chr12 26566549 26566649 -chr12 106703356 106718437 +chr12 26706109 26706130 +chr12 106703356 106718439 chr12 132242311 132242332 chr13 56380894 56381040 chr13 114073358 114074122 chr14 102919538 102919632 +chr15 31496974 31496995 +chr15 31637303 31637324 +chr15 40450778 40450800 +chr15 44117194 44117215 +chr15 44248462 44248483 chr15 74894096 74894117 chr16 1025231 1025252 chr16 49626994 49627100 @@ -27,38 +40,64 @@ chr17 31964205 32004138 chr17 77850848 77850938 chr17 83120464 83120485 chr17 83127668 83127689 +chr18 28481412 28481433 +chr18 28482559 28482580 chr18 70465189 70465210 chr18 78390326 78390347 chr19 395626 395835 chr19 3477781 3477868 chr19 29439299 29439424 chr19 38981201 38983536 +chr19 53185919 53185940 chr19 55068010 55068465 chr2 9737589 9737610 +chr2 80358794 80358815 chr2 138335007 138335083 chr2 157917136 157917157 chr2 238119351 238119427 +chr2 242182777 242182798 chr20 16410045 16410066 +chr20 25499107 25499128 chr20 38428231 38428252 +chr20 38430124 38430145 +chr20 62257534 62257555 +chr20 62378058 62378079 chr20 62755268 62755289 chr20 63443033 63443054 chr22 31903282 31903303 chr22 45328219 45328240 chr22 47732364 47732476 chr22 49494347 49494368 +chr3 11399 11532 chr3 112164423 112164444 +chr3 138126516 138126537 chr3 184714589 184714610 +chr3 192188379 192188404 chr4 1429347 1434609 chr4 8631479 8637158 +chr5 36023169 36023190 +chr5 39360014 39360035 chr5 71009525 71015235 +chr5 172418408 172418429 +chr5 172626365 172626386 chr5 176031036 176031057 +chr6 131707570 131707591 +chr6 157972782 157972814 +chr7 4824638 4824659 +chr7 7802502 7802523 chr7 23502979 23503000 chr7 68922678 68950323 chr7 75988853 75988924 +chr7 144186929 144186950 chr7 158151440 158151461 chr8 48193098 48193205 chr8 77023596 77040442 chr8 143669349 143669370 chr9 104414084 104414105 chr9 136535716 136535737 -chrX 125901244 125901387 \ No newline at end of file +chrX 90627638 90627659 +chrX 95207229 95207250 +chrX 95810791 95810812 +chrX 95812857 95812878 +chrX 125901244 125901387 +chrY 9591875 9591896 \ No newline at end of file diff --git a/repo_utils/answer_key/bench/bench_bnd/fn.vcf.gz b/repo_utils/answer_key/bench/bench_bnd/fn.vcf.gz index 91f1d940..6697a72e 100644 Binary files a/repo_utils/answer_key/bench/bench_bnd/fn.vcf.gz and b/repo_utils/answer_key/bench/bench_bnd/fn.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_bnd/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_bnd/fn.vcf.gz.tbi index d4b9963b..4a71391e 100644 Binary files a/repo_utils/answer_key/bench/bench_bnd/fn.vcf.gz.tbi and b/repo_utils/answer_key/bench/bench_bnd/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_bnd/fp.vcf.gz b/repo_utils/answer_key/bench/bench_bnd/fp.vcf.gz index 5f398605..52db73e2 100644 Binary files a/repo_utils/answer_key/bench/bench_bnd/fp.vcf.gz and b/repo_utils/answer_key/bench/bench_bnd/fp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_bnd/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_bnd/fp.vcf.gz.tbi index 3c488f5c..a0934eae 100644 Binary files a/repo_utils/answer_key/bench/bench_bnd/fp.vcf.gz.tbi and b/repo_utils/answer_key/bench/bench_bnd/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_bnd/log.txt b/repo_utils/answer_key/bench/bench_bnd/log.txt index 1bb3fa54..ece11b14 100644 --- a/repo_utils/answer_key/bench/bench_bnd/log.txt +++ b/repo_utils/answer_key/bench/bench_bnd/log.txt @@ -1,13 +1,13 @@ -2025-01-06 03:04:06,460 [INFO] Truvari v5.0.0 -2025-01-06 03:04:06,461 [INFO] Command /data/truvari/__main__.py bench -b repo_utils/test_files/variants/bnd.base.vcf.gz -c repo_utils/test_files/variants/bnd.comp.vcf.gz -p 0 -o test_results/bench_bnd/ --debug -2025-01-06 03:04:06,461 [INFO] Params: +2025-01-08 19:03:15,280 [INFO] Truvari v5.0.0 +2025-01-08 19:03:15,280 [INFO] Command /Users/english/code/truvari/truvari/__main__.py bench -b repo_utils/test_files/variants/bnd.base.vcf.gz -c repo_utils/test_files/variants/bnd.comp.vcf.gz -p 0 -o test_results/bench_bnd/ --no-decompose +2025-01-08 19:03:15,280 [INFO] Params: { - "base": "/data/repo_utils/test_files/variants/bnd.base.vcf.gz", - "comp": "/data/repo_utils/test_files/variants/bnd.comp.vcf.gz", + "base": "/Users/english/code/truvari/repo_utils/test_files/variants/bnd.base.vcf.gz", + "comp": "/Users/english/code/truvari/repo_utils/test_files/variants/bnd.comp.vcf.gz", "output": "test_results/bench_bnd/", "includebed": null, "extend": 0, - "debug": true, + "debug": false, "reference": null, "refdist": 500, "pctseq": 0.0, @@ -26,1118 +26,19 @@ "passonly": false, "no_ref": false, "pick": "single", + "ignore_monref": true, + "check_multi": true, "check_monref": true, - "check_multi": true + "no_single_bnd": true, + "write_resolved": false, + "decompose": false, + "short_circuit": false, + "skip_gt": false } -2025-01-06 03:04:06,497 [WARNING] Excluding 193 contigs present in comparison calls header but not baseline calls. -2025-01-06 03:04:06,500 [DEBUG] Comparing chunk 1 -2025-01-06 03:04:06,501 [DEBUG] All FP -> False None -> - None chr1 181146 severus_INS8023 N CGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCGCGCCGGCGCAGGCGCAGAGAGGCGCGCCG 36 PASS IMPRECISE;SVTYPE=INS;SVLEN=160;INSIDE_VNTR=TRUE;MAPQ=36;PHASESETID=171239;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:532:0.36:0,0,1:63:35 - -2025-01-06 03:04:06,502 [DEBUG] Comparing chunk 2 -2025-01-06 03:04:06,502 [DEBUG] All FP -> False None -> - None chr1 6005060 severus_DEL123 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=1600;END=6006660;STRANDS=+-;INSLEN=747;INSSEQ=None;MAPQ=60;PHASESETID=5144824;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:907:0.06:0,1,0:76:5 - -2025-01-06 03:04:06,503 [DEBUG] Comparing chunk 3 -2025-01-06 03:04:06,503 [DEBUG] Made mat -> True 100.0 -> - chr1 23272628 SV_1 G G]chr5:52747359] . PASS SVTYPE=BND;EVENTTYPE=TRA:UNBALANCED;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_171 GT:PSL:PSO 0/1:.:. - chr1 23272628 severus_BND164_1 N N]chr5:52747359] 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND164_2;STRANDS=++;MAPQ=60;PHASESETID=23220753|52503495;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:411:0.47:0,1,0:55:48 - -2025-01-06 03:04:06,505 [DEBUG] Comparing chunk 4 -2025-01-06 03:04:06,506 [DEBUG] Made mat -> True 66.66666666666666 -> - chr1 72195288 SV_2 T . SUBCLONAL SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-20211;END=72215499;SUBCLONAL=y;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr1 72195288 severus_DEL254 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=20211;END=72215499;STRANDS=+-;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/1:241:0.59:1,0,0:21:30 - -2025-01-06 03:04:06,507 [DEBUG] Comparing chunk 5 -2025-01-06 03:04:06,507 [DEBUG] All FP -> False None -> - None chr1 122627336 severus_BND3661_2 N N]chr2:80358805] 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND3661_1;STRANDS=++;INSLEN=92;INSSEQ=None;MAPQ=60;CLUSTERID=severus_4 GT:GQ:VAF:hVAF:DR:DV 0/1:209:0.5:1,0,0:29:29 - -2025-01-06 03:04:06,507 [DEBUG] Comparing chunk 6 -2025-01-06 03:04:06,508 [DEBUG] Made mat -> True 66.2824175580803 -> - chr1 151220118 SV_3 GCCTCAGTCTCCCGAGTAGCTGGGATTACAGGTGGTGTCATCATGCTTGGCTACTTTTTTGTATTTTTAGTAGAGACGGGGTTTCACCTTGCTAGCCAGGATGATCTCGATCTCCTGACCCTGTGATATGCCCACCTTGGCCTCCCCAAGTGCTGGGATTACAGGCATGAGCC G . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-172;END=151220290;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr1 151220118 severus_DEL361 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=173;END=151220291;STRANDS=+-;MAPQ=60;PHASESETID=150274906;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:603:0.32:0,1,0:80:37 - -2025-01-06 03:04:06,509 [DEBUG] Comparing chunk 7 -2025-01-06 03:04:06,509 [DEBUG] All FP -> False None -> - None chr1 224013772 severus_INS8772 N TGGAATGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGAATGGAATGGAATGGAATGGAATGGAATGGAGGAATTGGAATGGAATGGAATGGAATGGAATGGAATGGAATGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGAATGGAATGGAATGGAATGGATTGGAATGGAATGGAATGGATGGATGGAATGGAATGGAATGGAATGGAATGAATGGAATGGAATGGAATGGAATGGAATGGAATGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGATTGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGATGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAGAATGGAATGGAATGGAATGGAATGGAGATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGACTGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGATATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGGATGGAATGGATGGAATGGAATGGAGAAATGGAATGGATTGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGATGGAATGGAATGGAATGGAATGGAATGGAATGGAAGTGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAAGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGAATGGAATGGAATGGAATGGAATGGAATGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGAATGGAATGGAATGGAATGGAATGGAATGGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGATGGATGGAATGGAATGGAATGGAATGGAATGGAATGGAAATGGATGGAATGGCATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAAAATGGAATGGAATGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGGAATGAATGGAATGGAATGGAATGGAATGGACTCGAATGGAATGGAATGGAC 60 PASS PRECISE;SVTYPE=INS;SVLEN=2446;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=223776424;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:438:0.24:0,1,0:48:15 - -2025-01-06 03:04:06,510 [DEBUG] Comparing chunk 8 -2025-01-06 03:04:06,510 [DEBUG] All FP -> False None -> - None chr10 1238278 severus_INS8962 N CTCCCTCCGGTGTTTACTCCCCTCTCCCTCCCGGTGTTTACTCCCCCCCCTCTCCCTCCCGGTGTTTACTCCCCTCTCCCTCCCGGTGTTTACTCCCCCCTGCCTCCCGGTGTTTACTCCCCTCTCCCTCCCGGTGTTTACTCCCCTCTGCCTCCCGGTGTTTACTCCCCTCTGCCTCCCGGTGTTTACTCCCCTCTGCCTCCCGGTGTTTACTCCCTCTCCCTCCCGGTGTTTACTCCCCTCTGTCTCCCGGGTTTACTCCCCTCTGTCTCCCGGTGTTTACTCCCCTCTCCCTCCCGGTGTTTACTTTACTCCCCCCTGCCTCCCGGTGTTTACTCCCCTCTGCCTCCCGGTGTTTACTCCCCTCTGCCTCCCGGTGTTTACTCCCCCTGCCTCCCGGTGTTTACTCCCCTCTCCCCTCCCGGTGGGTGTTTACTCCCCTCTGCTTCCCCGGTGTTTACTCCCCTCTCCCTCCCGGTGTTTACTCCCCTCTGCCTCCCGGTGTTTACTCCCCTCTCCCTCCCGGTGTTTACTCCCCCCCTGCCTCCCGGTGTTTACTCCCCTCTCCCTCCCGGTGTTTACTCCCCTCTGCCTCCCGGTGTTTACTCCCCTCTCCCTCCCGGTGTTTACTCCCTCTCCCTCCCGGTGTTTACTCCCCCCTGCCTCCCGCCCTCTCCCTCCCGGTGTTTACTCCCCTCTCCCTCCCCGGTGTTTACTCCCCTCTCCCTCCCGGTGTTTACTCCCCTCTCCCTCCCGGTGTTTACTCCCCCCTGCCTCCCGGTGTTTACTCCCCTCTCCCTCCCGGTGTTTACTCCCTCTGCCTCCCGGTGTTTACTCCCCTCTCCCTCCCGGTGTTTACTCCCCTCTCCCTCCCGGTGTTTACTCCCC 60 PASS IMPRECISE;SVTYPE=INS;SVLEN=888;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=1110547;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:831:0.12:0,1,0:75:10 - -2025-01-06 03:04:06,511 [DEBUG] Comparing chunk 9 -2025-01-06 03:04:06,512 [DEBUG] Made mat -> True 66.65374802171124 -> - chr10 20233384 SV_79 G . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-5159;END=20238543;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=3;CIEND1=0;CIEND2=3;HOMLEN=3;HOMSEQ=GGC GT:PSL:PSO 0/1:.:. - chr10 20233384 severus_DEL701 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=5160;END=20238544;STRANDS=+-;MAPQ=60;PHASESETID=19396357;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:552:0.35:0,1,0:65:35 - -2025-01-06 03:04:06,513 [DEBUG] Comparing chunk 10 -2025-01-06 03:04:06,513 [DEBUG] Made mat -> True 66.21199171274466 -> - chr10 25515229 SV_80 C CAAAAGCCTTGTCATCTAGCATTAGGTATATCTCCCAATGCTATGATGACACATTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAATAAGAGAACAGGCCAGGCATGATGGCTGATGCCTATAGTCTCAGTGCTTTGGGAGGCTGAGATGAGAGGATTGCTTGAAGCCAGAAGTTCGAGACCAGCCTGAACAATACCGTGAGACCCTATCTCTACAAACAATAAAAATTATCTGGGTGTGGTGGCATATATTTGTAGTACTAGATACTTGAGAGACTGAAGAAGGAGGACCCCTTGAGCCCAGGAGTTTAAGGCTGCAGTGAGCTATGGTTGTGTCACTGCACTCCAAACAGAGGAAGGTCCTGTCTCTAATAACAATAATAAAAATAGAACTATTCAAATCAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . PASS SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=586;END=25515229;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=12;CIEND1=0;CIEND2=12;HOMLEN=12;HOMSEQ=AAAAGCCTTGTC GT:PSL:PSO 0/1:.:. - chr10 25515229 severus_INS9103 N AAAAGCCTTGTCATCTAGCATTAGGTATATCTCCCAATGCTATGATGACACATTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAATAAGAGAACAGGCCAGGCATGATGGCTGATGCCTATAGTCTCAGTGCTTTGGGAGGCTGAGATGAGAGGATTGCTTGAAGCCAGAAGTTCGAGACCAGCCTGAACAATACCGTGAGACCCTATCTCTACAAACAATAAAAATTATCTGGGTGTGGTGGCATATATTTGTAGTACTAGATACTTGAGAGACTGAAGAAGGAGGACCCCTTGAGCCCAGGAGTTTAAGGCTGCAGTGAGCTATGGTTGTGTCACTGCACTCCAAACAGAGGAAGGTCCTGTCTCTAATAACAATAATAAAAATAGAACTATTCAAATCAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 60 PASS PRECISE;SVTYPE=INS;SVLEN=582;MAPQ=60;PHASESETID=25433547;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:677:0.21:0,1,0:72:19 - -2025-01-06 03:04:06,514 [DEBUG] Comparing chunk 11 -2025-01-06 03:04:06,514 [DEBUG] All FP -> False None -> - None chr10 39478714 severus_INS9151 N AGTTTTTATATGAAGACATTTGCTTTTCCAACATAGCTAGCAAAGGGCTCAAAATATCCACTTGCAGATTCTTCAAAGGAGAGTTTCAAAACTGCTCAATCAAAATATAGGTGCAAATCTGTGACTTAATTGCATACATCACAAAGTAGTTTCTCAGAATGCTTCAGTGC 60 PASS PRECISE;SVTYPE=INS;SVLEN=170;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=38896646;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:920:0.05:0,1,0:76:4 - -2025-01-06 03:04:06,515 [DEBUG] Comparing chunk 12 -2025-01-06 03:04:06,515 [DEBUG] All FP -> False None -> - None chr10 67470511 severus_BND793_1 N N[chr10:68211499[ 60 PASS PRECISE;SVTYPE=BND;SVLEN=740988;MATE_ID=severus_BND793_2;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=67079858|68206942;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:629:0.3:0,0,1:80:34 - -2025-01-06 03:04:06,516 [DEBUG] Comparing chunk 13 -2025-01-06 03:04:06,516 [DEBUG] All FP -> False None -> - None chr10 68211499 severus_BND793_2 N ]chr10:67470511]N 60 PASS PRECISE;SVTYPE=BND;SVLEN=740988;MATE_ID=severus_BND793_1;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=67079858|68206942;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:629:0.3:0,0,1:80:34 - -2025-01-06 03:04:06,517 [DEBUG] Comparing chunk 14 -2025-01-06 03:04:06,517 [DEBUG] Made mat -> True 66.629619335845 -> - chr10 122835344 SV_85 T . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-1798;END=122837142;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=1;CIEND1=0;CIEND2=1;HOMLEN=1;HOMSEQ=T GT:PSL:PSO 0/1:.:. - chr10 122835344 severus_DEL886 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=1799;END=122837143;STRANDS=+-;MAPQ=60;PHASESETID=122220658;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:535:0.35:0,1,0:63:34 - -2025-01-06 03:04:06,518 [DEBUG] Comparing chunk 15 -2025-01-06 03:04:06,518 [DEBUG] Made mat -> True 66.35873584798317 -> - chr10 123543388 SV_86 AAGTGTTCAAATATTTTTAAAATGTTATGAAAACTGTGAACCCACAAATACAAGAAGCTCGATGAATCACAAGCAGAAGAAACATAAAGAAAATAAGACTTCATCATACCATATTCAAATTGCTTAAAATCAACAAAAAAGAGAAAACCCTCAAAGCAGCAGGGAAAAAAGACACAGTGTGTCCAAAAGGATCTTTCATTTGGCCTTTATGCTATT A . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-215;END=123543603;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=1;CIEND1=.;CIEND2=.;HOMLEN=1;HOMSEQ=A GT:PSL:PSO 0/1:.:. - chr10 123543388 severus_DEL887 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=216;END=123543604;STRANDS=+-;MAPQ=60;PHASESETID=123322268;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:526:0.37:0,0,1:72:43 - -2025-01-06 03:04:06,519 [DEBUG] Comparing chunk 16 -2025-01-06 03:04:06,519 [DEBUG] All FP -> False None -> - None chr10 132505652 severus_DEL950 N 60 PASS IMPRECISE;SVTYPE=DEL;SVLEN=760;END=132506412;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=132440526;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:428:0.39:0,0,1:52:33 - -2025-01-06 03:04:06,520 [DEBUG] Comparing chunk 17 -2025-01-06 03:04:06,521 [DEBUG] All FP -> False None -> - None chr11 964828 severus_INS9565 N GGAAATTAAAGGAAATAATCCCAGATGGAAGCGTGGAGATGGAAAGCATGGACGGGCGGGAAATTAAAGGAAATAATCCCAGATGGAAGCGTGGAGGTGGAAAGCATGGAACGGGCGGGAAATTAAAGGAAATAATCCCAGATGGAAGCGTGGAGGTGGAAGCATGGAACGGGCGGGAAATTAAAGGAAATAATCCCAGATGGAAGCGTGGAGATGGAAAGCATGGAACGGGCGGGAAATTAAAGGAAATAAATCCCAGATGGAAGCGTGGAGATGGAAAGCATGGAACGGGCG 60 PASS IMPRECISE;SVTYPE=INS;SVLEN=294;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=367049;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:933:0.06:0,0,1:78:5 - -2025-01-06 03:04:06,521 [DEBUG] Comparing chunk 18 -2025-01-06 03:04:06,522 [DEBUG] All FP -> False None -> - None chr11 33648576 severus_BND8004_2 N N[chrY:9591886[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND8004_1;STRANDS=+-;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/0:524:0.1:1,0,0:46:5 - -2025-01-06 03:04:06,522 [DEBUG] Comparing chunk 19 -2025-01-06 03:04:06,523 [DEBUG] Made mat -> True 65.90039220171883 -> - chr11 42923973 SV_88 C CATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTGGATTCAGTCATTTATTCATAAAGGTTAAGATTTGTATTTGCAATTATCAAATGTAGTTAAAAATAGAGCAACAAGCATTTAAAAATAACTTTTAAAAGCAACATAGTAAGTGGTTACATTTTGATGATCACAAATATATGCCTACATGACAATGAGAAGCCAACCACCTAATGTTGGCCAAATAAGTCCTTCTGGCCTGGCACAGCAGTTCCTGTTATCACATTGAACAGGGATTCAAAAACAGTGCTTCCCAAACAACTTGGAAGTGAGTCGAATGAGCCTAGAAAGCCATGTTAGGTGATTCAAATAGAAGTCAAGAAAAAATACATGTAAAGTGTTTGAATAAAATCATTTCAGGAAACAGAGTGGAAAAAATAATATTTTAATATTAAGATGTTATTTTAAATATAAATGAGTACCTGTATTAATAAATTAAATATCTGTTGACATTTGAATATCTCATCTATATTTCTAAAATATATAGAGATATAAAGAATTTTCAAATTGGCCAAACATATTTTTTGCTCTTAGTTGTCTTTTATTTAGGTATATGTGGTATATAGTATTATAAACATAATGGGGCATCACTTAAAAAGCAAAGACAAATAAATCATTCATAGCCTTTCAAAAGAAAGAAAAAAAAACACAGAGGCAGCCTGAATAGAATGGAGGAGGAGCCTGAAAAGCAACAGCCCATTTGCTGGAGCACTCATGGCAGATGAGCACGGTGTCTGGGATCTCAAGCTGTCCTGGTTCCAGCATCCCTCCCAGAACTCCCCTTGGGAACACGTTTTACACAAAGACCTTGTTTTCCCAATGTTATAGGTGCCCAATTCTTAATTAAATCATCTCTCACCCACAATAGCCTGTGGAGACCAATGATGCCTGTGGAGAAAGAACACTTTGTTGTGTCATGTTTTGTTTTGAACATCCCTGAAAGTCTAAAAAGAAGGCACCTGACAATCATTGTAAACTGGAAAAGCCAGAAAGAGGAAAAAATGGGCTCTTCAGATTCTGACTCTGTGTTTCAGGCTAAAGATTTCATTTCTACCTGAGATCATAGCATTTTGGAGCAAGGGGAATTCCTAGGGATTGTCTAGGATACACTTCTGGTTCAATACAGAAAAATAGGACGATATCCCTTTACACATTTTTTACTTGTGTTCCCAATAAGAGATATTTTCCTAGAAAAGCTTATCAGGCATTTTACCCAGGCTAAGTAGAACCAAAAGTTCTATTCTATTAATGTTAACATAAAGTTAAGTTTAGAGCTCTT . PASS SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=1333;END=42923973;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=6;CIEND1=0;CIEND2=6;HOMLEN=6;HOMSEQ=ATTCTT GT:PSL:PSO 0/1:.:. - chr11 42923973 severus_INS9752 N ATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTGGATTCAGTCATTTATTCATAAAGGTTAAGATTTGTATTTGCAATTATCAAATGTAGTTAAAAATAGAGCAACAAGCATTTAAAAATAACTTTTAAAAGCAACATAGTAAGTGGTTACATTTTGATGATCACAAATATATGCCTACATGACAATGAGAAGCCAACCACCTAATGTTGGCCAAATAAGTCCTTCTGGCCTGGCACAGCAGTTCCTGTTATCACATTGAACAGGGATTCAAAAACAGTGCTTCCCAAACAACTTGGAAGTGAGTCGAATGAGCCTAGAAAGCCATGTTAGGTGATTCAAATAGAAGTCAAGAAAAAATACATGTAAAGTGTTTGAATAAAATCATTTCAGGAAACAGAGTGGAAAAAATAATATTTTAATATTAAGATGTTATTTTAAATATAAATGAGTACCTGTATTAATAAATTAAATATCTGTTGACATTTGAATATCTCATCTATATTTCTAAAATATATAGAGATATAAAGAATTTTCAAATTGGCCAAACATATTTTTTGCTCTTAGTTGTCTTTTATTTAGGTATATGTGGTATATAGTATTATAAACATAATGGGGCATCACTTAAAAAGCAAAGACAAATAAATCATTCATAGCCTTTCAAAAGAAAGAAAAAAAAACACAGAGGCAGCTGAATAGAATGGAGGAGGAGCCTGAAAAGCAACAGCCCATTTGCTGGAGCACTCATGGCAGATGAGCACGGTGTCTGGGATCTCAAGCTGTCCTGGTTCCAGCATCCCTCCCAGAACCTCCCCTTGGGAACACGTTTTACACAAAGACCTTGTTTTCCCAATGTTATAGGTGCCCAATTCTTAATTAAATCATCTCTCACCCACAATAGCCTGTGGAGACCAATGATGCCTGTGGAGAAAGAACACTTTGTTGTGTCATGTTTTGTTTTGAACATCCCTGAAAGTCTAAAAAGAAGGCACCTGACAATCATTGTAAACTGGAAAAGCCAGAAAGAGGAAAAAATGGGCTCTTCAGATTCTGACTCTGTGTTTCAGGCTAAAGATTTCATTTCTACCTGAGATCATAGCATTTTGGAGCAAGGGGAATTCCTAGGGATTGTCTAGGATACACTTCTGGTTCAATACAGAAAAATAGGACGATATCCCTTTACACATTTTTTACTTGTGTTCCCAATAAGAGATATTTTCCTAGAAAAGCTTATCAGGCATTTTACCCAGGCTAAGTAGAACCAAAAGTTCTATTCTATTAATGTTAACATAAAGTTAAGTTTAGAGCTCTT 60 PASS PRECISE;SVTYPE=INS;SVLEN=1348;ALINGED_POS=chr11:58759701-58761049;MAPQ=60;PHASESETID=42671579;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:667:0.26:0,1,0:111:39 - -2025-01-06 03:04:06,524 [DEBUG] Comparing chunk 20 -2025-01-06 03:04:06,525 [DEBUG] All FP -> False None -> - None chr11 44662936 severus_INS9761 N CCCCTCCCCCTCCCCCCTCCCCCTCCCCCTCCCCCTCCCCCTCCCCTCCCCT 60 PASS PRECISE;SVTYPE=INS;SVLEN=52;MAPQ=60;PHASESETID=44661675;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:639:0.1:0,0,1:56:6 - -2025-01-06 03:04:06,525 [DEBUG] Comparing chunk 21 -2025-01-06 03:04:06,525 [DEBUG] All FP -> False None -> - None chr11 48880466 severus_INV1136 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=19495;STRANDS=++;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/0:984:0.06:1,0,0:82:5 - -2025-01-06 03:04:06,526 [DEBUG] Comparing chunk 22 -2025-01-06 03:04:06,526 [DEBUG] All FP -> False None -> - None chr11 48888300 severus_INV1138 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=3827;STRANDS=++;MAPQ=60;PHASESETID=46838236;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:895:0.08:0,1,0:77:7 - -2025-01-06 03:04:06,527 [DEBUG] Comparing chunk 23 -2025-01-06 03:04:06,527 [DEBUG] All FP -> False None -> - None chr11 68232234 severus_INV1185 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=821;STRANDS=++;DETAILED_TYPE=inv_tra;MAPQ=60;PHASESETID=68002185;HP=1;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:437:0.44:0,1,0:75:59 - -2025-01-06 03:04:06,528 [DEBUG] Made mat -> True 99.0 -> - chr11 68232231 SV_90 A [chr3:192188396[A . PASS SVTYPE=BND;EVENTTYPE=TRA:BALANCED;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=3;CIEND1=-3;CIEND2=0;HOMLEN=3;HOMSEQ=TGG;MATEID=SV_27;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,2 - chr11 68232231 severus_BND1184_1 N [chr3:192188394[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1184_2;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:398:0.53:1,0,0:52:59 - -2025-01-06 03:04:06,528 [DEBUG] chr11 68232231 SV_90 A [chr3:192188396[A . PASS SVTYPE=BND;EVENTTYPE=TRA:BALANCED;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=3;CIEND1=-3;CIEND2=0;HOMLEN=3;HOMSEQ=TGG;MATEID=SV_27;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,2 - and chr11 68233077 severus_BND1186_1 N N[chr3:192188390[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1186_2;STRANDS=-+;MAPQ=60;PHASESETID=68002185|190937960;HP=1;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:455:0.69:0,1,0:23:52 - BND POS not within BNDDIST -2025-01-06 03:04:06,528 [DEBUG] Made mat -> False None -> - chr11 68232231 SV_90 A [chr3:192188396[A . PASS SVTYPE=BND;EVENTTYPE=TRA:BALANCED;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=3;CIEND1=-3;CIEND2=0;HOMLEN=3;HOMSEQ=TGG;MATEID=SV_27;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,2 - chr11 68233077 severus_BND1186_1 N N[chr3:192188390[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1186_2;STRANDS=-+;MAPQ=60;PHASESETID=68002185|190937960;HP=1;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:455:0.69:0,1,0:23:52 - -2025-01-06 03:04:06,529 [DEBUG] chr11 68232232 SV_91 T T]chr11:68233057] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_92;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,1 - and chr11 68232231 severus_BND1184_1 N [chr3:192188394[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1184_2;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:398:0.53:1,0,0:52:59 - BND join CHROM -2025-01-06 03:04:06,529 [DEBUG] Made mat -> False None -> - chr11 68232232 SV_91 T T]chr11:68233057] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_92;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,1 - chr11 68232231 severus_BND1184_1 N [chr3:192188394[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1184_2;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:398:0.53:1,0,0:52:59 - -2025-01-06 03:04:06,530 [DEBUG] chr11 68232232 SV_91 T T]chr11:68233057] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_92;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,1 - and chr11 68233077 severus_BND1186_1 N N[chr3:192188390[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1186_2;STRANDS=-+;MAPQ=60;PHASESETID=68002185|190937960;HP=1;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:455:0.69:0,1,0:23:52 - BND POS not within BNDDIST -2025-01-06 03:04:06,530 [DEBUG] Made mat -> False None -> - chr11 68232232 SV_91 T T]chr11:68233057] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_92;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,1 - chr11 68233077 severus_BND1186_1 N N[chr3:192188390[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1186_2;STRANDS=-+;MAPQ=60;PHASESETID=68002185|190937960;HP=1;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:455:0.69:0,1,0:23:52 - -2025-01-06 03:04:06,531 [DEBUG] chr11 68233057 SV_92 C C]chr11:68232232] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_91;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,1 - and chr11 68232231 severus_BND1184_1 N [chr3:192188394[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1184_2;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:398:0.53:1,0,0:52:59 - BND POS not within BNDDIST -2025-01-06 03:04:06,531 [DEBUG] Made mat -> False None -> - chr11 68233057 SV_92 C C]chr11:68232232] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_91;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,1 - chr11 68232231 severus_BND1184_1 N [chr3:192188394[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1184_2;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:398:0.53:1,0,0:52:59 - -2025-01-06 03:04:06,531 [DEBUG] chr11 68233057 SV_92 C C]chr11:68232232] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_91;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,1 - and chr11 68233077 severus_BND1186_1 N N[chr3:192188390[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1186_2;STRANDS=-+;MAPQ=60;PHASESETID=68002185|190937960;HP=1;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:455:0.69:0,1,0:23:52 - BND join CHROM -2025-01-06 03:04:06,532 [DEBUG] Made mat -> False None -> - chr11 68233057 SV_92 C C]chr11:68232232] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_91;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,1 - chr11 68233077 severus_BND1186_1 N N[chr3:192188390[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1186_2;STRANDS=-+;MAPQ=60;PHASESETID=68002185|190937960;HP=1;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:455:0.69:0,1,0:23:52 - -2025-01-06 03:04:06,532 [DEBUG] chr11 68233078 SV_93 A ]chr3:192188390]TA . PASS SVTYPE=BND;EVENTTYPE=TRA:BALANCED;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_26;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,.:.,. - and chr11 68232231 severus_BND1184_1 N [chr3:192188394[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1184_2;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:398:0.53:1,0,0:52:59 - BND POS not within BNDDIST -2025-01-06 03:04:06,532 [DEBUG] Made mat -> False None -> - chr11 68233078 SV_93 A ]chr3:192188390]TA . PASS SVTYPE=BND;EVENTTYPE=TRA:BALANCED;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_26;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,.:.,. - chr11 68232231 severus_BND1184_1 N [chr3:192188394[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1184_2;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:398:0.53:1,0,0:52:59 - -2025-01-06 03:04:06,533 [DEBUG] chr11 68233078 SV_93 A ]chr3:192188390]TA . PASS SVTYPE=BND;EVENTTYPE=TRA:BALANCED;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_26;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,.:.,. - and chr11 68233077 severus_BND1186_1 N N[chr3:192188390[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1186_2;STRANDS=-+;MAPQ=60;PHASESETID=68002185|190937960;HP=1;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:455:0.69:0,1,0:23:52 - BND strand/direction mismatch -2025-01-06 03:04:06,533 [DEBUG] Made mat -> False None -> - chr11 68233078 SV_93 A ]chr3:192188390]TA . PASS SVTYPE=BND;EVENTTYPE=TRA:BALANCED;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_26;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,.:.,. - chr11 68233077 severus_BND1186_1 N N[chr3:192188390[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1186_2;STRANDS=-+;MAPQ=60;PHASESETID=68002185|190937960;HP=1;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:455:0.69:0,1,0:23:52 - -2025-01-06 03:04:06,534 [DEBUG] Comparing chunk 24 -2025-01-06 03:04:06,535 [DEBUG] All FP -> False None -> - None chr11 80583412 severus_INS9917 N ATATAAATATAAATATATAAATATAAATATTTATATAGATATAAATATAAAT 60 PASS IMPRECISE;SVTYPE=INS;SVLEN=52;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=80208246;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:1125:0.07:0,0,1:96:7 - -2025-01-06 03:04:06,535 [DEBUG] Comparing chunk 25 -2025-01-06 03:04:06,536 [DEBUG] Made mat -> True 66.6552423384761 -> - chr11 95796274 SV_95 C . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-5834;END=95802108;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=2;CIEND1=0;CIEND2=2;HOMLEN=2;HOMSEQ=TG GT:PSL:PSO 0/1:.:. - chr11 95796274 severus_DEL1240 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=5835;END=95802109;STRANDS=+-;MAPQ=60;PHASESETID=95758794;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:641:0.29:0,0,1:96:39 - -2025-01-06 03:04:06,537 [DEBUG] Comparing chunk 26 -2025-01-06 03:04:06,537 [DEBUG] All FP -> False None -> - None chr11 105902633 severus_INV1264 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=535;STRANDS=++;DETAILED_TYPE=inv_tra;MAPQ=60;PHASESETID=105786144;HP=2;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:376:0.52:0,0,1:48:51 - -2025-01-06 03:04:06,537 [DEBUG] chr11 105902632 SV_96 G G]chr11:105903169] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=-1;CIPOS2=1;CIEND1=-1;CIEND2=1;HOMLEN=2;HOMSEQ=GC;MATEID=SV_179;CLUSTERID=cluster_4 GT:PSL:PSO 0|1:.,chr6*157972805*1:.,2 - and chr11 105902637 severus_BND1265_1 N [chr6:157972804[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1265_2;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:453:0.68:1,0,0:24:52 - BND join CHROM -2025-01-06 03:04:06,538 [DEBUG] Made mat -> False None -> - chr11 105902632 SV_96 G G]chr11:105903169] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=-1;CIPOS2=1;CIEND1=-1;CIEND2=1;HOMLEN=2;HOMSEQ=GC;MATEID=SV_179;CLUSTERID=cluster_4 GT:PSL:PSO 0|1:.,chr6*157972805*1:.,2 - chr11 105902637 severus_BND1265_1 N [chr6:157972804[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1265_2;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:453:0.68:1,0,0:24:52 - -2025-01-06 03:04:06,538 [DEBUG] Made mat -> True 99.0 -> - chr11 105902638 SV_178 A [chr6:157972805[A . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=1;CIEND1=.;CIEND2=.;HOMLEN=1;HOMSEQ=G;MATEID=SV_56;CLUSTERID=cluster_4 GT:PSL:PSO 0|1:.,chr6*157972805*1:.,1 - chr11 105902637 severus_BND1265_1 N [chr6:157972804[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1265_2;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:453:0.68:1,0,0:24:52 - -2025-01-06 03:04:06,539 [DEBUG] chr11 105903169 SV_179 G G]chr11:105902632] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=-1;CIPOS2=1;CIEND1=-1;CIEND2=1;HOMLEN=2;HOMSEQ=GC;MATEID=SV_96;CLUSTERID=cluster_4 GT:PSL:PSO 0|1:.,chr6*157972805*1:.,2 - and chr11 105902637 severus_BND1265_1 N [chr6:157972804[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1265_2;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:453:0.68:1,0,0:24:52 - BND POS not within BNDDIST -2025-01-06 03:04:06,539 [DEBUG] Made mat -> False None -> - chr11 105903169 SV_179 G G]chr11:105902632] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=-1;CIPOS2=1;CIEND1=-1;CIEND2=1;HOMLEN=2;HOMSEQ=GC;MATEID=SV_96;CLUSTERID=cluster_4 GT:PSL:PSO 0|1:.,chr6*157972805*1:.,2 - chr11 105902637 severus_BND1265_1 N [chr6:157972804[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1265_2;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:453:0.68:1,0,0:24:52 - -2025-01-06 03:04:06,540 [DEBUG] Comparing chunk 27 -2025-01-06 03:04:06,540 [DEBUG] chr11 125661474 SV_177 G ]chr6:157972793]G . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_54;CLUSTERID=cluster_4 GT:PSL:PSO 0/1:.:. - and chr11 125661473 severus_BND1296_1 N N[chr6:157972793[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1296_2;STRANDS=-+;MAPQ=60;PHASESETID=125584229|157821672;HP=2;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:541:0.69:0,0,1:28:62 - BND strand/direction mismatch -2025-01-06 03:04:06,541 [DEBUG] Made mat -> False None -> - chr11 125661474 SV_177 G ]chr6:157972793]G . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_54;CLUSTERID=cluster_4 GT:PSL:PSO 0/1:.:. - chr11 125661473 severus_BND1296_1 N N[chr6:157972793[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1296_2;STRANDS=-+;MAPQ=60;PHASESETID=125584229|157821672;HP=2;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:541:0.69:0,0,1:28:62 - -2025-01-06 03:04:06,541 [DEBUG] Comparing chunk 28 -2025-01-06 03:04:06,542 [DEBUG] Made mat -> True 66.2931810097713 -> - chr11 130986347 SV_97 CAAGACCCATCAGTGTGCTGTATTCAGGAAACCCATCTCACGTGCAGAGACACACATAGGCTCAAAATAAAAGGATGGAGGAAGATCTACCAAGCAAATGGAAAACAAAAAAAGGCAGGAATTGCAATCCTAGTCTCTGATAAAACAGACTTTAAACCAACAAAGATTAAAAGAGACA C . SUBCLONAL SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-177;END=130986524;SUBCLONAL=u;COMPLEX=n;CIPOS1=0;CIPOS2=4;CIEND1=.;CIEND2=.;HOMLEN=4;HOMSEQ=AAGA GT:PSL:PSO 0/1:.:. - chr11 130986347 severus_DEL1305 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=178;END=130986525;STRANDS=+-;MAPQ=60;PHASESETID=129955810;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:552:0.35:0,0,1:123:67 - -2025-01-06 03:04:06,543 [DEBUG] Comparing chunk 29 -2025-01-06 03:04:06,543 [DEBUG] All FP -> False None -> - None chr11 135076382 severus_BND4588_2 N N]chr3:11410] 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND4588_1;STRANDS=++;MAPQ=60;PHASESETID=10253|0;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:256:0.29:1,0,0:29:12 - -2025-01-06 03:04:06,543 [DEBUG] Comparing chunk 30 -2025-01-06 03:04:06,544 [DEBUG] All FP -> False None -> - None chr12 2572365 severus_INS10171 N CTTCCTCTTCCTGCTCCTTCTCCTCTTCTCCTCCTCCCTTCCTCTCTCCTCTTCCTCTCTCCTCC 60 PASS IMPRECISE;SVTYPE=INS;SVLEN=69;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=2346545;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:639:0.12:0,1,0:58:8 - -2025-01-06 03:04:06,544 [DEBUG] Comparing chunk 31 -2025-01-06 03:04:06,545 [DEBUG] Made mat -> True 66.66666666666666 -> - chr12 7380776 SV_99 G GGGACTGTGGTGGGGTAGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACACATTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAAGAAAGAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . PASS SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=216;END=7380776;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr12 7380776 severus_INS10199 N GGACTGTGGTGGGGTAGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACACATTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAAGAAAGAAAAAGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 60 PASS PRECISE;SVTYPE=INS;SVLEN=216;MAPQ=60;PHASESETID=7355130;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:565:0.34:0,1,0:132:68 - -2025-01-06 03:04:06,545 [DEBUG] Comparing chunk 32 -2025-01-06 03:04:06,546 [DEBUG] All FP -> False None -> - None chr12 10429008 severus_DEL1386 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=15423;END=10444431;STRANDS=+-;MAPQ=60;PHASESETID=10169923;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:1086:0.06:0,1,0:91:6 - -2025-01-06 03:04:06,546 [DEBUG] Comparing chunk 33 -2025-01-06 03:04:06,547 [DEBUG] Made mat -> True 65.16853932584269 -> - chr12 16630818 SV_100 T TAAAGATCATGATGTGGTAATGGGGATATGCTGGAGAAACTAAAGCTTTGTATGGAGAGTAGAACAGCCTTGGGACAGCTGAGCATTTGGACTGCCTCAAATGAGGAATTTGGAATTTAAAGAAAGAAGGTGTTTAATAAATATTTGTTGAATGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . PASS SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=267;END=16630818;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=9;CIEND1=0;CIEND2=9;HOMLEN=9;HOMSEQ=AAAGATCAT GT:PSL:PSO 0/1:.:. - chr12 16630818 severus_INS10236 N AAAGATCATGATGTGGTAATGGGGATATGCTGGAGAAACTAAAGCTTTGTATGGAGAGTAGAACAGCCTTGGGACAGCTGAGCATTTGGACTGCCTCAAATGAGGAATTTGGAATTTAAAGAAAGAAGGTGTTTAATAAATATTTGTTGAATGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 60 PASS PRECISE;SVTYPE=INS;SVLEN=261;MAPQ=60;PHASESETID=16585186;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:616:0.31:0,0,1:120:53 - -2025-01-06 03:04:06,548 [DEBUG] Comparing chunk 34 -2025-01-06 03:04:06,548 [DEBUG] All FP -> False None -> - None chr12 24759758 severus_BND1426_1 N N[chr12:26706120[ 60 PASS PRECISE;SVTYPE=BND;SVLEN=1946362;MATE_ID=severus_BND1426_2;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=24667139|26380438;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:616:0.3:0,1,0:138:60 - -2025-01-06 03:04:06,548 [DEBUG] Comparing chunk 35 -2025-01-06 03:04:06,549 [DEBUG] All FP -> False None -> - None chr12 26566560 severus_DEL1431 N 60 PASS IMPRECISE;SVTYPE=DEL;SVLEN=79;END=26566639;STRANDS=+-;MAPQ=60;PHASESETID=26380438;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:1150:0.05:0,1,0:128:7 - -2025-01-06 03:04:06,549 [DEBUG] Comparing chunk 36 -2025-01-06 03:04:06,549 [DEBUG] All FP -> False None -> - None chr12 26706120 severus_BND1426_2 N ]chr12:24759758]N 60 PASS PRECISE;SVTYPE=BND;SVLEN=1946362;MATE_ID=severus_BND1426_1;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=24667139|26380438;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:616:0.3:0,1,0:138:60 - -2025-01-06 03:04:06,550 [DEBUG] Comparing chunk 37 -2025-01-06 03:04:06,551 [DEBUG] Made mat -> True 65.79516974253816 -> - chr12 40668214 SV_102 ATTGCAGTGCAATAAATGCACTGAAGTGGGGAAGAGAAAGCTGCCCTTTTACCCCTCTTGTTGTGTCCTATGTAGC A . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-75;END=40668289;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=2;CIEND1=.;CIEND2=.;HOMLEN=2;HOMSEQ=TT GT:PSL:PSO 0/1:.:. - chr12 40668214 severus_DEL1461 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=76;END=40668290;STRANDS=+-;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/1:386:0.49:1,0,0:62:59 - -2025-01-06 03:04:06,551 [DEBUG] Comparing chunk 38 -2025-01-06 03:04:06,552 [DEBUG] Made mat -> True 66.53721682847896 -> - chr12 83211411 SV_105 TGT TTAAGGCTGCAGTGAGCTATGGTTGTGTCACTGCACTCCAAACAGAGGAAGGTCCTGTCTCTAATAACAATAATAAAAATAGAACTATTCAAATCAAGAAATATCAAGTGTTTGTGTGGAATGCAACTTAAGCTCAATATTATAATGTCACACAGAATGGCATGAAGGCAATTAGGCCAGGGTCCGGGGGCGAGGGTGACTTCAGCTAGGCTTTGAAGAATGATTCAGATTTGAATTGGTGGAGGAAAAAGGGAAGATCATTTCAGGCAAAATGAGTAAAAATATGGAAATAGGAAGAATCCTGGATGGAAAATGAGATGTGGTAATGGGGATATGCTGGAGAAACTAAAGCTTTGTATGGAGAGTAGAACAGCCTTGGGACAGCTGAGCATTTGGACTGCCTCAAATGAGGAATTTGGAATTTAAAGAAAGAAGGTGTTTAATAAATATTTGTTGAATGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . PASS SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=512;END=83211413;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr12 83211411 severus_INS10422 N TAAGGCTGCAGTGAGCTATGGTTGTGTCACTGCACTCCAAACAGAGGAAGGTCCTGTCTCTAATAACAATAATAAAAATAGAACTATTCAAATCAAGAAATATCAAGTGTTTGTGTGGAATGCAACTTAAGCTCAATATTATAATGTCACACAGAATGGCATGAAGGCAATTAGGCCAGGGTCCGGGGGCGAGGGTGACTTCAGCTAGGCTTTGAAGAATGATTCAGATTTGAATTGGTGGAGGAAAAAGGGAAGATCATTTCAGGCAAAATGAGTAAAAATATGGAAATAGGAAGAATCCTGGATGGAAAATGAGATGTGGTAATGGGGATAATGCTGGAGAAACTAAAGCTTTGTATGGAGAGTAGAACAGCCTTGGGACAGCTGAGCATTTGGACTGCCTCAAATGAGGAATTTGGAATTTAAAGAAGAAGGTGTTTAATAAATATTTGTTGAATGAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 60 PASS PRECISE;SVTYPE=INS;SVLEN=512;MAPQ=60;PHASESETID=82963796;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:366:0.49:0,1,0:50:48 - -2025-01-06 03:04:06,553 [DEBUG] Comparing chunk 39 -2025-01-06 03:04:06,554 [DEBUG] All FN -> False None -> - chr12 106703367 SV_106 A . PASS SVTYPE=DUP;EVENTTYPE=DUP:TANDEM;SVLEN=15060;END=106718427;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=2;CIEND1=0;CIEND2=2;HOMLEN=2;HOMSEQ=TG GT:PSL:PSO 0/1:.:. - None -2025-01-06 03:04:06,554 [DEBUG] All FP -> False None -> - None chr12 106703369 severus_BND1576_1 N N[chr12:106718429[ 60 PASS PRECISE;SVTYPE=BND;SVLEN=15060;MATE_ID=severus_BND1576_2;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/1:411:0.46:0,1,1:67:58 - -2025-01-06 03:04:06,555 [DEBUG] All FP -> False None -> - None chr12 106718429 severus_BND1576_2 N ]chr12:106703369]N 60 PASS PRECISE;SVTYPE=BND;SVLEN=15060;MATE_ID=severus_BND1576_1;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=106598184;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:411:0.46:0,1,1:67:58 - -2025-01-06 03:04:06,556 [DEBUG] Comparing chunk 40 -2025-01-06 03:04:06,556 [DEBUG] chr12 121442781 SV_107 C ]chr15:40450789]GC . COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=n;COMPLEX=u;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr12 121442780 severus_BND2220_2 N N[chr15:40450789[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2220_1;STRANDS=+-;DETAILED_TYPE=Reciprocal_tra;MAPQ=60;PHASESETID=40436746|121363378;HP=1;CLUSTERID=severus_6 GT:GQ:VAF:hVAF:DR:DV 0/1:354:0.55:0,1,0:38:46 - BND strand/direction mismatch -2025-01-06 03:04:06,556 [DEBUG] Made mat -> False None -> - chr12 121442781 SV_107 C ]chr15:40450789]GC . COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=n;COMPLEX=u;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr12 121442780 severus_BND2220_2 N N[chr15:40450789[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2220_1;STRANDS=+-;DETAILED_TYPE=Reciprocal_tra;MAPQ=60;PHASESETID=40436746|121363378;HP=1;CLUSTERID=severus_6 GT:GQ:VAF:hVAF:DR:DV 0/1:354:0.55:0,1,0:38:46 - -2025-01-06 03:04:06,557 [DEBUG] Made mat -> True 99.5 -> - chr12 121442781 SV_107 C ]chr15:40450789]GC . COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=n;COMPLEX=u;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr12 121442781 severus_BND2221_2 N ]chr15:40450790]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2221_1;STRANDS=-+;DETAILED_TYPE=Reciprocal_tra;MAPQ=60;PHASESETID=40436746|121363378;HP=1;CLUSTERID=severus_6 GT:GQ:VAF:hVAF:DR:DV 0/1:398:0.44:0,1,0:51:40 - -2025-01-06 03:04:06,557 [DEBUG] Made mat -> True 96.5 -> - chr12 121442783 SV_108 G G[chr15:40450793[ . COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=n;COMPLEX=u;CIPOS1=-2;CIPOS2=2;CIEND1=.;CIEND2=.;HOMLEN=4;HOMSEQ=GGAG GT:PSL:PSO 0/1:.:. - chr12 121442780 severus_BND2220_2 N N[chr15:40450789[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2220_1;STRANDS=+-;DETAILED_TYPE=Reciprocal_tra;MAPQ=60;PHASESETID=40436746|121363378;HP=1;CLUSTERID=severus_6 GT:GQ:VAF:hVAF:DR:DV 0/1:354:0.55:0,1,0:38:46 - -2025-01-06 03:04:06,557 [DEBUG] chr12 121442783 SV_108 G G[chr15:40450793[ . COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=n;COMPLEX=u;CIPOS1=-2;CIPOS2=2;CIEND1=.;CIEND2=.;HOMLEN=4;HOMSEQ=GGAG GT:PSL:PSO 0/1:.:. - and chr12 121442781 severus_BND2221_2 N ]chr15:40450790]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2221_1;STRANDS=-+;DETAILED_TYPE=Reciprocal_tra;MAPQ=60;PHASESETID=40436746|121363378;HP=1;CLUSTERID=severus_6 GT:GQ:VAF:hVAF:DR:DV 0/1:398:0.44:0,1,0:51:40 - BND strand/direction mismatch -2025-01-06 03:04:06,558 [DEBUG] Made mat -> False None -> - chr12 121442783 SV_108 G G[chr15:40450793[ . COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=n;COMPLEX=u;CIPOS1=-2;CIPOS2=2;CIEND1=.;CIEND2=.;HOMLEN=4;HOMSEQ=GGAG GT:PSL:PSO 0/1:.:. - chr12 121442781 severus_BND2221_2 N ]chr15:40450790]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2221_1;STRANDS=-+;DETAILED_TYPE=Reciprocal_tra;MAPQ=60;PHASESETID=40436746|121363378;HP=1;CLUSTERID=severus_6 GT:GQ:VAF:hVAF:DR:DV 0/1:398:0.44:0,1,0:51:40 - -2025-01-06 03:04:06,559 [DEBUG] Comparing chunk 41 -2025-01-06 03:04:06,559 [DEBUG] All FP -> False None -> - None chr12 132242322 severus_INS10651 N TCCCTATACCCATTACACACACGCCACACCCCCTTCCCGGAGCCCTCCCTATACCCATTACACACACACCACACCCCCTTCCCGGGGCCCTCCCTATACCCATTACACACACGCCACACCCCCTTCCCGGAGCCCTCCCTATACCCATTACACACACGCCACACCCCCTTCCAGGGGCCCTCCCTATACCCATTACACACACAACACACCCCCTTCCCGGGGCCTTCCCTATACCCATTACACACACGCCACACCCCCTTCCAGGGGCCCTCCCTATACCCATTACACACACAACACACCCCCTTCCCGGGGCCTTCCCTATACCCATTACACACACGCCACACCCCCTTCCAGGGGCCCTCCCTATACCCATTACACACACGCCACACCCCCTTCCCGGGGCCCTCCCTATACCCATTACACACACAACACACACACTTCCCGGAGCCCTCCCTATACCCATTACACACACGCCACACACCCTTCCAGGGGCCCTCCCTATACCCATTACACACACAACACACCCCCTTCCCGGGGCCTTCCCTATACCCATTACACACACGCCACACCCCCTCCAGGGGCCCTCCCTATACCCATTACACACACGCCACACCCCCTTCCCAGGGCCCTCCCTATACCCATTACACACACGCCACACCCCCTTCCAGGGGCCCTCCCTATACCCATTACACACACAACACACCCCCTTCCCGGGCCCTCCCTATACCCATTACACACACGCCACACCCCCTTCCCGGAGCCCTCCCTATACCCATTACACACACGCCACACCCCCTTCCGGGGCCCTCCCTATACCCATTACACACACAACACACACACTTCCCGGAGCCCTCCCTATACCCATTACACACACGCCACACACCCTTCCAGGGGCCCTCCCTATACCCATTAGACACACAACACACCCCCTTCCCGGGGCCCTCCCTATACCCATTACACACACAACACACACTTCCCGGGGCCCTCCCTATACCCATTACACACACGCCACACCCCCTTCCAGGGGCCCTCCCTATACCCATTACACACACGCCACACCCCCTTCCCAGGGCCCTCCCTATACCCATTACACACACAACACACACCCTTCCCGGAGCCCCCCCTATACCCATTACACACACGCCACACCCCCTTCCAGGGGCCCTCCCTATACCCATTACACACACAACACACCCCCTTCCCGGGGCCCTCCCTATACCCATTACACACACAACACACACCCTTCCAGGGGCCCTCCCTATACCCATTACACACACGCCACACCCCTTCCCGGGGCCCTCCCTATACCCATTACACACACACACACCCCCTTCCCGGGGCCCTCCCTATACCCATTACACACACAACACACCCCCTTCCCGGGGCCCTCCCTATCCCCATTACACACACAACACACCCCCTTCCCGGGGCCCTCCCTATACCCATTACACACACACCACACCCCCTTTCCCGGGGCCCTCCCTATACCCATTACACACACGCCACACACCCTTCCAGGGGCCCTCCATATACCCATTTACACACACGCCACGCCCCTTCCCGGGGCCCTCCCTATACCCATTACACACACGCCACACCCCCTTCCCGGGTCCCTCCCTACACCCATTACACACACACCACACACCCTTCCAGGGGCCCTCCCTATACCCATTAACACACACGCCACGCCCCCTTCCCGGGCCCTTCCTATACCCATTACACACACGCCACACCCCATTCCCGGGGCCCTCCCTATACCCATTACACACACACCACACACCCTTCCCGGGGCCCTCCCTATACCCATTAGACACACACCACACACCCTTCCCCGGGCCCTCCCTATACCCATTAGACACACGCCACACACCCTTCCAGGGGCCCTCCCTATACCCATTACACACACGCCACACACCCTATCCCAGGGCCGTCCCTATACCCATTACACACACAACACACACCCTTCCAGGGGCCCTCCCTGTACCCATTACACACACAACACACACTTCCCGGGGCCCTCCCTATACCCATTACATACACAACACACCCCCTTCCTGGGGCCCTCCCTATACCCATTACACACACAACACACACACTTCCCGGGGCCCTCCCTATACCCATTACACACACACAACACCCCCTTCCCAGGGACCCTCCCTATACCCATTACACACACAACACCCCCTTCCCAGGGACCCTCCCTATACCCATTACACACACAACACACCCTTCCCGGGTCCTCCCTATACCCATTACACACACAACACACACTTCCCGGGGCCCTCCCCTATACCCATTACACACACAACACACCCCCCTTCCTGGGGCCCTCCCTATACCCATTACACACACAACACACACACTTCCCGGGGCCCTCCCTATACCCATTACACACACACAACACCCCCTTCCCAGGGACCCTCCCTATACCCATTACACACACAACACCCCCCTTCCCAGGGACCCTCCCTATACCCATTACACACACAACACCCCCTTCCCAGGGACCCTCCCTATACCCATTACACACACACAACACCCCCTTCCAGGGACCCTCCCTATACCCATTACACACACAACACCCCCTTCCCAGGGACCCTCCCTATACCCATTACACACACAACACACCCCCTTCCTGGGGCCGTCCCTATACCCATTACACACATACCACACACCCTTCCAGGGGCCCTCATACCCATTACACACACAAACACACCCCCTTCCTGGGGCCGCCCATTACACACACGCCACACCCCCTTCCCGGGCCCTCCCTATCCCCATTAAACACACAACACACACCCTTCCCGGGGCCCTCCCTATACCCATTACACACACAACACACACTTCCCGGGGCCCTCCCTATCCCCATTAAACACACAACACACCCCCTTCCCGGGGCCCTCCCTATACCCATTACACACACGCCACACACCCTTCCCGGGGCCGTCCCTATACCCATTAAACACACAACACACCCCCTTCCCGGGGCCCTCCCTATCCCCATTAAACACACAACACACCCCTTCCCAGGGCCCTCCCTATACCCATTACACACACAACACACACTTCCCGGGCCCTCCCTATACCCATTACACACACGCCACACACCCTTCCCGGGGCCCTCCCTATACCCATTACACACACGCCACACCCCCTTCCCGGGGCCCTCCCTATACCCATTACACACACACCACACCCCCTTCCCGGGGCCCTCCCTATACCCATTACACACACAACACACACCCTTCCCGGGGCCCTCCCTATACCCATTACACACACGCCACACCCCCTTCCCGGGGCCCTCCCTATACCCATTACACACACGCCACACACCCTTCCCGGGGCCCTCCCTATACCCATTACACACACAACACACACCCTTCCGGGGCCCTCCCTATACCCATTACACACACACCACACCCCCTTCCCGGGGCCCTCCCTATACCCATACACACACAACACACCCCCTTCCCGGGGCCTTCCCTATACCCATTACACACACGCCACACCCCCTTCCAGGGGCCCTCCCTATACCCATTACACACACACACACCCCCTTCCCCGGGGCCCTCCCTATACCCATTACACACACGCCACACCCCCTTCCCGGAGCCCTCCCTATACCCATTACACACACACCACACCCCCTTCCAGGGGCCCTCCCTATACCCATTACACACACAACACACACCCTTCCCGGGGCCCTCCCTATCCCCATTACACACACACCACACACCCTTCCCGGGGCCCTCCCTATACCATTACACACACGCCACACCCCCTTCCCGGGGGCCCTCCCTATACCCATTACACACACGCCACACCCCTTCCCGGGGCCCTCCCTATACCCATTACACACACGCACACCCCCTTCCCGGGGCCCTCCCTATA 60 PASS IMPRECISE;SVTYPE=INS;SVLEN=3891;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=0;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:460:0.09:0,1,0:40:4 - -2025-01-06 03:04:06,560 [DEBUG] Comparing chunk 42 -2025-01-06 03:04:06,561 [DEBUG] Made mat -> True 66.62469834858565 -> - chr13 39536625 SV_110 T . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-1587;END=39538212;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=3;CIEND1=0;CIEND2=3;HOMLEN=3;HOMSEQ=CTC GT:PSL:PSO 0/1:.:. - chr13 39536625 severus_DEL1744 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=1588;END=39538213;STRANDS=+-;MAPQ=60;PHASESETID=39504403;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:616:0.31:0,1,0:119:53 - -2025-01-06 03:04:06,561 [DEBUG] Comparing chunk 43 -2025-01-06 03:04:06,562 [DEBUG] All FN -> False None -> - chr13 56380905 SV_111 C . SUBCLONAL-COMPLEX SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-125;END=56381030;SUBCLONAL=y;COMPLEX=u;CIPOS1=0;CIPOS2=2;CIEND1=0;CIEND2=2;HOMLEN=2;HOMSEQ=GG GT:PSL:PSO 0/1:.:. - None -2025-01-06 03:04:06,562 [DEBUG] Comparing chunk 44 -2025-01-06 03:04:06,563 [DEBUG] Made mat -> True 66.58222500307498 -> - chr13 84309984 SV_113 TCCTCCAGACCCCAGAATGGTGGATCCACTGACAGCTTGCACCATGCGCCTGGAAAAGCCACAGAGACTCAATGCCAGCCTGTGAAAACAGCCAGGAGGGGGGCTATGCTCTGCAAATCCACAGGGGCGAAGCTGCCCAAGACTATGGGAACCTATCTCTTGCATCAGGGTGACCTGGATGTGAGACATGGCATCAAAAGAGATCACTTTGGAGCTTTAGAATTTTACTGCCCTGCTGGATTTTGAACTTGCGTGGACCCTGTATCCCCTTTGTATTGGTCAAATTCTCCCATTTGGAATGGCTGTATTTACCCAATACCTGTACCTCCGTTGCATCTAGGAAGTAAGTAGCTTTCTTTTGATATTACAGGCTCATAGGCAGAAGGGACTTGCCTTGTCTCAGATGAGACTTTGGACTGTGGACTTTTGGGTTAATGCTGAAATGAGTTTAAGACTTTGGGAGACTGTTGGGAAGGCATGACTGGTTTTGAAATGTGAAGACATGAGATTTAGAGGGGTCAGGGTGGAATTATATGGTGTGGCTCTGTGTCCCCACCCAAATTTCATCTTGAATCATACTCTCATCATTCCCACATGTTGTGGGAGGGATCCAGTGGGAGATAATTTGAATCATGGGGGCGGTTTCCCCCGTACTGTTCTCATGGTAGTGAATAAGTCTCATGAGATCTGATGATTTTATCAGTAGTTTCCACTTTTGCATCTCTCCCATTTTTTCTCTTGTCATCGCCATGCAAGAAGTGCCTTTCACCTCCCGCAATGATTCTGAGG T . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-788;END=84310772;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=5;CIEND1=.;CIEND2=.;HOMLEN=5;HOMSEQ=CCTCC GT:PSL:PSO 0/1:.:. - chr13 84309984 severus_DEL1839 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=789;END=84310773;STRANDS=+-;MAPQ=60;PHASESETID=84123424;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:603:0.32:0,1,0:112:52 - -2025-01-06 03:04:06,564 [DEBUG] Comparing chunk 45 -2025-01-06 03:04:06,564 [DEBUG] All FP -> False None -> - None chr13 114073369 severus_DEL1952 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=743;END=114074112;STRANDS=+-;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/0:780:0.1:1,0,0:69:8 - -2025-01-06 03:04:06,565 [DEBUG] Comparing chunk 46 -2025-01-06 03:04:06,565 [DEBUG] Made mat -> True 100.0 -> - chr13 114353244 SV_172 T T]chr3:139976414] . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=1;CIEND1=.;CIEND2=.;HOMLEN=1;HOMSEQ=G;MATEID=SV_20;CLUSTERID=cluster_3 GT:PSL:PSO 1|0:chr13*114353244*1,.:1,. - chr13 114353244 severus_BND1960_1 N N]chr3:139976414] 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1960_2;STRANDS=++;MAPQ=60;PHASESETID=0|139256694;HP=2;CLUSTERID=severus_2 GT:GQ:VAF:hVAF:DR:DV 0/1:424:0.45:0,0,1:75:62 - -2025-01-06 03:04:06,566 [DEBUG] Comparing chunk 47 -2025-01-06 03:04:06,566 [DEBUG] Made mat -> True 65.63301282051283 -> - chr14 60918508 SV_115 AATTGTTCATTTTTACATGATTTTCTCCCTTCCAAATACCTTTATGTGGACACTTGCCAATATC A . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-63;END=60918571;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=3;CIEND1=.;CIEND2=.;HOMLEN=3;HOMSEQ=ATT GT:PSL:PSO 0/1:.:. - chr14 60918508 severus_DEL2045 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=64;END=60918572;STRANDS=+-;MAPQ=60;PHASESETID=60834923;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:526:0.38:0,0,1:109:66 - -2025-01-06 03:04:06,567 [DEBUG] Comparing chunk 48 -2025-01-06 03:04:06,568 [DEBUG] Made mat -> True 66.54217231599014 -> - chr14 60923413 SV_116 TATTATACATATTTAACAAAAATGCTTCTGTTACATTTGCTACCTGTCTTAACCTACTATATCTTATCTTTACATTTTATACTTTACATTAATACTTTAAATGATACATGTTTATCCATTGCATCATTTACAGTATTTCATAACATAATTTATTTAACCAGTCTTCAATTAGACATTTAGGTCAGTTTTCATTTGTTGTTTTTATAAATAGAATCTTGCTAAATTTTTATGTGATCTTCTAATTATTTCATTAGCAAAAAATCCCTGGATTAACGGATGGACATGGCATGGCACGGTGGCTCACGCCTGTAATCCCAGTACTTTGAGAGGCTGAGGCAGGCGGATTACTTGAGGCCAGGAGTTTGAGACCAGCTTGGGCAATATGGTGGAACCTTGTTTCCACAAAAAATAAAAAAAATTAGCCAGGTGTGGTGGTGTGCATCTGTAATCCCAGCTACTCTGCAGGCTGAGAACCCAGGACTGCACTCCAACCTGGATGACAGAGCGAGACTGTCTTAAAACAAAACAAAACAAG T . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-534;END=60923947;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=2;CIEND1=.;CIEND2=.;HOMLEN=2;HOMSEQ=AT GT:PSL:PSO 0/1:.:. - chr14 60923413 severus_DEL2046 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=535;END=60923948;STRANDS=+-;MAPQ=60;PHASESETID=60834923;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:654:0.27:0,1,0:99:37 - -2025-01-06 03:04:06,569 [DEBUG] Comparing chunk 49 -2025-01-06 03:04:06,569 [DEBUG] All FP -> False None -> - None chr14 102919549 severus_DEL2141 N 60 PASS IMPRECISE;SVTYPE=DEL;SVLEN=73;END=102919622;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=102154200;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:920:0.05:0,0,1:76:4 - -2025-01-06 03:04:06,570 [DEBUG] Comparing chunk 50 -2025-01-06 03:04:06,570 [DEBUG] All FP -> False None -> - None chr15 31496985 severus_BND2200_1 N N[chr15:31637314[ 60 PASS PRECISE;SVTYPE=BND;SVLEN=140329;MATE_ID=severus_BND2200_2;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=30577380;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:603:0.31:0,0,1:111:51 - -2025-01-06 03:04:06,571 [DEBUG] Comparing chunk 51 -2025-01-06 03:04:06,571 [DEBUG] All FP -> False None -> - None chr15 31637314 severus_BND2200_2 N ]chr15:31496985]N 60 PASS PRECISE;SVTYPE=BND;SVLEN=140329;MATE_ID=severus_BND2200_1;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=30577380;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:603:0.31:0,0,1:111:51 - -2025-01-06 03:04:06,571 [DEBUG] Comparing chunk 52 -2025-01-06 03:04:06,572 [DEBUG] All FP -> False None -> - None chr15 40450789 severus_BND2220_1 N ]chr12:121442780]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2220_2;STRANDS=+-;DETAILED_TYPE=Reciprocal_tra;MAPQ=60;PHASESETID=40436746|121363378;HP=1;CLUSTERID=severus_6 GT:GQ:VAF:hVAF:DR:DV 0/1:354:0.55:0,1,0:38:46 - -2025-01-06 03:04:06,572 [DEBUG] All FP -> False None -> - None chr15 40450790 severus_BND2221_1 N N[chr12:121442781[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2221_2;STRANDS=-+;DETAILED_TYPE=Reciprocal_tra;MAPQ=60;PHASESETID=40436746|121363378;HP=1;CLUSTERID=severus_6 GT:GQ:VAF:hVAF:DR:DV 0/1:398:0.44:0,1,0:51:40 - -2025-01-06 03:04:06,572 [DEBUG] Comparing chunk 53 -2025-01-06 03:04:06,573 [DEBUG] All FP -> False None -> - None chr15 44117205 severus_BND2229_1 N N[chr15:44248473[ 60 PASS PRECISE;SVTYPE=BND;SVLEN=131268;MATE_ID=severus_BND2229_2;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/0:1048:0.09:1,0,0:110:11 - -2025-01-06 03:04:06,573 [DEBUG] Comparing chunk 54 -2025-01-06 03:04:06,574 [DEBUG] All FP -> False None -> - None chr15 44248473 severus_BND2229_2 N ]chr15:44117205]N 60 PASS PRECISE;SVTYPE=BND;SVLEN=131268;MATE_ID=severus_BND2229_1;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=44087788;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:1048:0.09:1,0,0:110:11 - -2025-01-06 03:04:06,574 [DEBUG] Comparing chunk 55 -2025-01-06 03:04:06,574 [DEBUG] All FP -> False None -> - None chr15 74894107 severus_INS11615 N GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTTTTCTGAGCCAG 60 PASS PRECISE;SVTYPE=INS;SVLEN=174;MAPQ=60;PHASESETID=74814372;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:780:0.19:0,1,0:80:19 - -2025-01-06 03:04:06,575 [DEBUG] Comparing chunk 56 -2025-01-06 03:04:06,576 [DEBUG] Made mat -> True 66.56820914627052 -> - chr15 79431718 SV_121 T . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-1015;END=79432733;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr15 79431717 severus_DEL2314 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=1014;END=79432731;STRANDS=+-;MAPQ=60;PHASESETID=79268433;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:741:0.16:0,1,0:72:14 - -2025-01-06 03:04:06,577 [DEBUG] Comparing chunk 57 -2025-01-06 03:04:06,577 [DEBUG] All FP -> False None -> - None chr16 1025242 severus_INS11797 N 60 PASS PRECISE;SVTYPE=INS;SVLEN=481;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=944364;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:332:0.09:0,0,1:29:3 - -2025-01-06 03:04:06,578 [DEBUG] Comparing chunk 58 -2025-01-06 03:04:06,578 [DEBUG] All FP -> False None -> - None chr16 49627005 severus_DEL2501 N 60 PASS IMPRECISE;SVTYPE=DEL;SVLEN=85;END=49627090;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=49451070;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:1035:0.05:0,1,0:86:5 - -2025-01-06 03:04:06,579 [DEBUG] Comparing chunk 59 -2025-01-06 03:04:06,579 [DEBUG] Made mat -> True 66.27334957651699 -> - chr16 50928456 SV_125 N . COMPLEX SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=168;END=50928624;SUBCLONAL=n;COMPLEX=u;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr16 50928456 severus_DEL2506 N 60 PASS IMPRECISE;SVTYPE=DEL;SVLEN=169;END=50928625;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=50077877;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:539:0.36:0,0,1:118:67 - -2025-01-06 03:04:06,580 [DEBUG] Comparing chunk 60 -2025-01-06 03:04:06,581 [DEBUG] Made mat -> True 65.82805907172997 -> - chr16 89166442 SV_127 CGATCTGCTGGGGACACAGACCCACGCAGCAGGGGAGAGGACAGACGTCCGGAACTGGGTAGAGATGGGCCGTGGGTGG C . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-78;END=89166520;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=64;CIEND1=.;CIEND2=.;HOMLEN=64;HOMSEQ=GATCTGCTGGGGACACAGACCCACGCAGCAGGGGAGAGGACAGACGTCCGGAACTGGGTAGAGA GT:PSL:PSO 0/1:.:. - chr16 89166442 severus_DEL2614 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=79;END=89166521;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=88425074;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:565:0.34:0,0,1:75:39 - -2025-01-06 03:04:06,581 [DEBUG] Comparing chunk 61 -2025-01-06 03:04:06,582 [DEBUG] All FP -> False None -> - None chr16 89536470 severus_INS12139 N GTGAGGCCGGGTGAGGCGGGCGAGGCGGGCGAGGCCAGGTGAGGCAGGTGAGGTGAGGCGGGTGAGGTCAGGTGAGGCAGGTGAG 60 PASS IMPRECISE;SVTYPE=INS;SVLEN=85;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=89181254;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:1150:0.05:0,0,1:95:5 - -2025-01-06 03:04:06,582 [DEBUG] Comparing chunk 62 -2025-01-06 03:04:06,583 [DEBUG] chr17 31964216 SV_128 T . SUBCLONAL-COMPLEX SVTYPE=DUP;EVENTTYPE=DUP:TANDEM;SVLEN=13253;END=31977469;SUBCLONAL=y;COMPLEX=u;CIPOS1=0;CIPOS2=21;CIEND1=0;CIEND2=21;HOMLEN=21;HOMSEQ=GGGTTTCACCGTGTTAGCCAG GT:PSL:PSO 0/1:.:. - and chr17 31977413 severus_DEL2767 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=26715;END=32004128;STRANDS=+-;MAPQ=60;PHASESETID=30925135;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:341:0.46:0,1,0:45:39 - are not the same SVTYPE -2025-01-06 03:04:06,583 [DEBUG] chr17 31964216 SV_128 T . SUBCLONAL-COMPLEX SVTYPE=DUP;EVENTTYPE=DUP:TANDEM;SVLEN=13253;END=31977469;SUBCLONAL=y;COMPLEX=u;CIPOS1=0;CIPOS2=21;CIEND1=0;CIEND2=21;HOMLEN=21;HOMSEQ=GGGTTTCACCGTGTTAGCCAG GT:PSL:PSO 0/1:.:. - and chr17 31977413 severus_DEL2767 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=26715;END=32004128;STRANDS=+-;MAPQ=60;PHASESETID=30925135;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:341:0.46:0,1,0:45:39 - size similarity is too low (0.496) -2025-01-06 03:04:06,583 [DEBUG] Made mat -> False 16.60739642703484 -> - chr17 31964216 SV_128 T . SUBCLONAL-COMPLEX SVTYPE=DUP;EVENTTYPE=DUP:TANDEM;SVLEN=13253;END=31977469;SUBCLONAL=y;COMPLEX=u;CIPOS1=0;CIPOS2=21;CIEND1=0;CIEND2=21;HOMLEN=21;HOMSEQ=GGGTTTCACCGTGTTAGCCAG GT:PSL:PSO 0/1:.:. - chr17 31977413 severus_DEL2767 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=26715;END=32004128;STRANDS=+-;MAPQ=60;PHASESETID=30925135;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:341:0.46:0,1,0:45:39 - -2025-01-06 03:04:06,584 [DEBUG] Made mat -> True 66.66666666666666 -> - chr17 31977413 SV_129 G . SUBCLONAL-COMPLEX SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-26715;END=32004128;SUBCLONAL=y;COMPLEX=u;CIPOS1=0;CIPOS2=1;CIEND1=0;CIEND2=1;HOMLEN=1;HOMSEQ=G GT:PSL:PSO 0/1:.:. - chr17 31977413 severus_DEL2767 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=26715;END=32004128;STRANDS=+-;MAPQ=60;PHASESETID=30925135;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:341:0.46:0,1,0:45:39 - -2025-01-06 03:04:06,584 [DEBUG] All FP -> False None -> - None chr17 31964314 severus_BND2766_1 N N[chr17:31977567[ 60 PASS PRECISE;SVTYPE=BND;SVLEN=13253;MATE_ID=severus_BND2766_2;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/0:485:0.07:1,0,0:41:3 - -2025-01-06 03:04:06,585 [DEBUG] All FP -> False None -> - None chr17 31977567 severus_BND2766_2 N ]chr17:31964314]N 60 PASS PRECISE;SVTYPE=BND;SVLEN=13253;MATE_ID=severus_BND2766_1;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=30925135;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:485:0.07:1,0,0:41:3 - -2025-01-06 03:04:06,586 [DEBUG] Comparing chunk 63 -2025-01-06 03:04:06,586 [DEBUG] Made mat -> True 33.319846550489636 -> - chr17 32670397 SV_131 A . COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=7415;END=32677812;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr17 32670397 severus_INV2772 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=7411;STRANDS=++;DETAILED_TYPE=dup_inv_segment;MAPQ=60;PHASESETID=32034272;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:386:0.49:0,0,1:62:59 - -2025-01-06 03:04:06,587 [DEBUG] Comparing chunk 64 -2025-01-06 03:04:06,588 [DEBUG] All FN -> False None -> - chr17 39887391 SV_132 N N]chrUn_KI270744v1:120025] . COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - None -2025-01-06 03:04:06,588 [DEBUG] Comparing chunk 65 -2025-01-06 03:04:06,589 [DEBUG] Made mat -> True 66.66112473501681 -> - chr17 53933117 SV_133 C . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-12028;END=53945145;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=4;CIEND1=0;CIEND2=4;HOMLEN=4;HOMSEQ=TCTA GT:PSL:PSO 0/1:.:. - chr17 53933117 severus_DEL2823 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=12029;END=53945146;STRANDS=+-;MAPQ=60;PHASESETID=53146798;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:373:0.51:0,0,1:95:99 - -2025-01-06 03:04:06,589 [DEBUG] Comparing chunk 66 -2025-01-06 03:04:06,590 [DEBUG] All FP -> False None -> - None chr17 77850859 severus_DEL2878 N 60 PASS IMPRECISE;SVTYPE=DEL;SVLEN=69;END=77850928;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=77458493;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:907:0.06:0,0,1:76:5 - -2025-01-06 03:04:06,590 [DEBUG] Comparing chunk 67 -2025-01-06 03:04:06,590 [DEBUG] All FP -> False None -> - None chr17 83120475 severus_INS12591 N CCTGTGCGCTCCCCTGTGTGCTGCCCTGTGCGCTCCCCTGTGCCCTCCCCTGTGCGCTGCCCTGTGCGCTGCCCTGTGCGCTCCCCTGTGCGCTGCCCTGTGCGCTGCCCTGTGCGCTCCCCTGTGCGCTCCCCTGTGCGCTGC 60 PASS PRECISE;SVTYPE=INS;SVLEN=144;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=82714311;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:434:0.16:0,0,1:42:8 - -2025-01-06 03:04:06,591 [DEBUG] Comparing chunk 68 -2025-01-06 03:04:06,591 [DEBUG] All FP -> False None -> - None chr17 83127679 severus_INS12592 N GTAGGGTGGGTGTGGGATCTGTAGGGTGGGTGTGGGATTGTAGGGTGGGTGTGGGATTGTAGGGTGGGTGTGGGATCTGTAGGGTGGGTGCAGGATCTGTAGGGTGGGTGTGGGATTGTAGGGTGGGTGTGGGATCTGTAGGGTGGGTGTGGGATTGTAGGGTGGGTGTGGGATCTGTAGGGTGGGTGTGGGATCTGTAGGGTGGGTGTGGGATT 60 PASS PRECISE;SVTYPE=INS;SVLEN=215;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=82714311;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:690:0.05:0,0,1:57:3 - -2025-01-06 03:04:06,592 [DEBUG] Comparing chunk 69 -2025-01-06 03:04:06,593 [DEBUG] Made mat -> True 99.5 -> - chr18 21493609 SV_136 T [chr20:25499118[N . COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=n;COMPLEX=u;CIPOS1=0;CIPOS2=0;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr18 21493610 severus_BND2983_1 N [chr20:25499118[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2983_2;STRANDS=--;MAPQ=60;PHASESETID=20911267|25143452;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:411:0.46:0,1,0:58:50 - -2025-01-06 03:04:06,594 [DEBUG] Comparing chunk 70 -2025-01-06 03:04:06,595 [DEBUG] chr18 28481424 SV_138 N N[chrX:95810802[ . COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=n;COMPLEX=u;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr18 28481423 severus_BND2998_1 N ]chrX:95812868]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2998_2;STRANDS=+-;DETAILED_TYPE=Reciprocal_tra;MAPQ=60;CLUSTERID=severus_7 GT:GQ:VAF:hVAF:DR:DV 0/1:361:0.55:1,0,0:39:47 - BND join POS not within BNDDIST -2025-01-06 03:04:06,595 [DEBUG] Made mat -> False None -> - chr18 28481424 SV_138 N N[chrX:95810802[ . COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=n;COMPLEX=u;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr18 28481423 severus_BND2998_1 N ]chrX:95812868]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2998_2;STRANDS=+-;DETAILED_TYPE=Reciprocal_tra;MAPQ=60;CLUSTERID=severus_7 GT:GQ:VAF:hVAF:DR:DV 0/1:361:0.55:1,0,0:39:47 - -2025-01-06 03:04:06,596 [DEBUG] Comparing chunk 71 -2025-01-06 03:04:06,596 [DEBUG] All FP -> False None -> - None chr18 28482570 severus_BND2999_1 N N[chrX:95810802[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2999_2;STRANDS=-+;DETAILED_TYPE=Reciprocal_tra;MAPQ=60;CLUSTERID=severus_7 GT:GQ:VAF:hVAF:DR:DV 0/1:324:0.53:1,0,0:38:43 - -2025-01-06 03:04:06,597 [DEBUG] Comparing chunk 72 -2025-01-06 03:04:06,597 [DEBUG] All FP -> False None -> - None chr18 70465200 severus_INS12822 N TGTGGTGTGTGTGTGTGTGGTGTGTGTGTGGTGTATGTGTATGTGTGGTGTGTGTGTGTATGTGTGTACGTGTGGTGTGTGTATGTGTGGTGTGTGTGTGTATGTGTGTATGTGTGGTGTATGTGTGGTGTGTATGTATGTGTGTATGTGTGGTGTGTGTGTGTATGTGTGTATGTGTGGTGTGTGTGGTGTGTGTGTGGTGTGTGTGTATGTGGTGTGTGTGTGGTGTGTGGCTGTGTGTGTGTACGTGGGGTGTATGTGTGGTGTGTGCATGTGTGTATGTGTGGTGTGTGTATGTGGTGTGTGTGTGGTGTGTGGTGTGTGTGTATGTGTGTATGTGTGGTGTGTGTGTGGTGTGTGGCTGTGTGTGTGTACGTGGTATGTGTGTGTATGTGTGGTGTGTGTATGTGTGGTGTGTGTGTGTATGTGGTGTGTGTGTGGTGTGTGGCTGTGTGTGTGTACGTGGGGTGTGTGTGTATGTGTGGTGTGTGTGTGTATGTGTGTATGTGTGGTGTGTGTGTGGTGTGCGTGTATGTGTGTATGTGGTATGTGTGTGGTGTGTGGCTGCGTATGTGTGGTGTGTGGCTGTGTGTGTGTTGTACGTGGGGTGTGTGTGTGTATGTGTGTATGTGTGGTGTGTGTATATGTGTGGTGTGTATGTGTGGTGTGTGTATGTGTGGTGTGTG 60 PASS PRECISE;SVTYPE=INS;SVLEN=686;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=69712280;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:498:0.07:0,1,0:42:3 - -2025-01-06 03:04:06,598 [DEBUG] Comparing chunk 73 -2025-01-06 03:04:06,598 [DEBUG] All FP -> False None -> - None chr18 78390337 severus_INS12874 N AGAGAGAGGGAGGAGGGGGAGGAGAGGGAAAGGGAGAAAAGGGAGGGAGAGAGAGGATAGGAGAGAGAGGGAGGAGAGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGGAGAGAGAGGAGGGGAGAGAGGGAGGAGGGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGGGAGAGAGAGGGAGGAGGGGGAAGAGAGGGAAAGGGAGAAAAGGGAGGGAGAGAGAGGATAGGAGAGAGAGGAAGGAGAGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGGGGAAGAGAGGGAGGAGGGGGAAGAGAGGGAAAGGGAGAAAAGGGAGGGAGAGAGAGGATAGGAGAGAGAGGAAGGAGAGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGGAAGAGAGAGGAGGACAGGAGAGAGAGGAGGAGGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGAGGAGAGAGGGAGGAGGAGGAAGAGAGGGAAAGGGAGAAAAGGGAGGGAGAGAGAGGACAGGAGAGAGAGGAAGGAGAGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGAAGAGAGAGGAGGACAGGAGAGAGAGGGAGGAGGGAGAGAGAGGAGGACAGGAGA 60 PASS PRECISE;SVTYPE=INS;SVLEN=953;MAPQ=60;PHASESETID=77721785;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:289:0.44:0,1,0:37:29 - -2025-01-06 03:04:06,598 [DEBUG] Comparing chunk 74 -2025-01-06 03:04:06,599 [DEBUG] All FP -> False None -> - None chr19 395637 severus_DEL3171 N 60 PASS IMPRECISE;SVTYPE=DEL;SVLEN=188;END=395825;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=62632;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:383:0.08:0,0,1:33:3 - -2025-01-06 03:04:06,599 [DEBUG] Comparing chunk 75 -2025-01-06 03:04:06,599 [DEBUG] All FP -> False None -> - None chr19 3477792 severus_DEL3209 N 60 PASS IMPRECISE;SVTYPE=DEL;SVLEN=66;END=3477858;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=3045591;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:601:0.06:0,0,1:50:3 - -2025-01-06 03:04:06,600 [DEBUG] Comparing chunk 76 -2025-01-06 03:04:06,600 [DEBUG] Made mat -> True 66.63695450288091 -> - chr19 4856356 SV_139 A . SUBCLONAL-COMPLEX SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-4485;END=4860841;SUBCLONAL=y;COMPLEX=u;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr19 4856356 severus_DEL3219 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=4487;END=4860843;STRANDS=+-;MAPQ=60;PHASESETID=4319360;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:537:0.08:0,0,1:46:4 - -2025-01-06 03:04:06,601 [DEBUG] Comparing chunk 77 -2025-01-06 03:04:06,602 [DEBUG] Made mat -> True 66.59655580386486 -> - chr19 11196184 SV_140 G . SUBCLONAL-COMPLEX SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=22820;END=11219004;SUBCLONAL=u;COMPLEX=y;CIPOS1=0;CIPOS2=11;CIEND1=0;CIEND2=11;HOMLEN=11;HOMSEQ=AGTAGCTGGGA GT:PSL:PSO 0/1:.:. - chr19 11196136 severus_DUP3242 N 60 PASS PRECISE;SVTYPE=DUP;SVLEN=22820;END=11218956;STRANDS=-+;DETAILED_TYPE=tandem_duplication;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:378:0.26:0,0,1:42:15 - -2025-01-06 03:04:06,602 [DEBUG] chr19 11196184 SV_140 G . SUBCLONAL-COMPLEX SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=22820;END=11219004;SUBCLONAL=u;COMPLEX=y;CIPOS1=0;CIPOS2=11;CIEND1=0;CIEND2=11;HOMLEN=11;HOMSEQ=AGTAGCTGGGA GT:PSL:PSO 0/1:.:. - and chr19 11207621 severus_INV3243 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=62;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:247:0.39:0,0,1:30:19 - are not the same SVTYPE -2025-01-06 03:04:06,603 [DEBUG] chr19 11196184 SV_140 G . SUBCLONAL-COMPLEX SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=22820;END=11219004;SUBCLONAL=u;COMPLEX=y;CIPOS1=0;CIPOS2=11;CIEND1=0;CIEND2=11;HOMLEN=11;HOMSEQ=AGTAGCTGGGA GT:PSL:PSO 0/1:.:. - and chr19 11207621 severus_INV3243 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=62;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:247:0.39:0,0,1:30:19 - size similarity is too low (0.003) -2025-01-06 03:04:06,603 [DEBUG] Made mat -> False 0.09202447587015884 -> - chr19 11196184 SV_140 G . SUBCLONAL-COMPLEX SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=22820;END=11219004;SUBCLONAL=u;COMPLEX=y;CIPOS1=0;CIPOS2=11;CIEND1=0;CIEND2=11;HOMLEN=11;HOMSEQ=AGTAGCTGGGA GT:PSL:PSO 0/1:.:. - chr19 11207621 severus_INV3243 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=62;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:247:0.39:0,0,1:30:19 - -2025-01-06 03:04:06,603 [DEBUG] chr19 11196184 SV_140 G . SUBCLONAL-COMPLEX SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=22820;END=11219004;SUBCLONAL=u;COMPLEX=y;CIPOS1=0;CIPOS2=11;CIEND1=0;CIEND2=11;HOMLEN=11;HOMSEQ=AGTAGCTGGGA GT:PSL:PSO 0/1:.:. - and chr19 11208275 severus_INV3244 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=9528;STRANDS=--;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:365:0.28:0,0,1:41:16 - are not the same SVTYPE -2025-01-06 03:04:06,604 [DEBUG] chr19 11196184 SV_140 G . SUBCLONAL-COMPLEX SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=22820;END=11219004;SUBCLONAL=u;COMPLEX=y;CIPOS1=0;CIPOS2=11;CIEND1=0;CIEND2=11;HOMLEN=11;HOMSEQ=AGTAGCTGGGA GT:PSL:PSO 0/1:.:. - and chr19 11208275 severus_INV3244 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=9528;STRANDS=--;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:365:0.28:0,0,1:41:16 - size similarity is too low (0.418) -2025-01-06 03:04:06,604 [DEBUG] Made mat -> False 13.91907676918012 -> - chr19 11196184 SV_140 G . SUBCLONAL-COMPLEX SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=22820;END=11219004;SUBCLONAL=u;COMPLEX=y;CIPOS1=0;CIPOS2=11;CIEND1=0;CIEND2=11;HOMLEN=11;HOMSEQ=AGTAGCTGGGA GT:PSL:PSO 0/1:.:. - chr19 11208275 severus_INV3244 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=9528;STRANDS=--;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:365:0.28:0,0,1:41:16 - -2025-01-06 03:04:06,604 [DEBUG] chr19 11207621 SV_141 C . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=62;END=11207683;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr19 11196136 severus_DUP3242 N 60 PASS PRECISE;SVTYPE=DUP;SVLEN=22820;END=11218956;STRANDS=-+;DETAILED_TYPE=tandem_duplication;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:378:0.26:0,0,1:42:15 - are not the same SVTYPE -2025-01-06 03:04:06,605 [DEBUG] chr19 11207621 SV_141 C . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=62;END=11207683;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr19 11196136 severus_DUP3242 N 60 PASS PRECISE;SVTYPE=DUP;SVLEN=22820;END=11218956;STRANDS=-+;DETAILED_TYPE=tandem_duplication;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:378:0.26:0,0,1:42:15 - size similarity is too low (0.003) -2025-01-06 03:04:06,605 [DEBUG] Made mat -> False 0.1825843403224908 -> - chr19 11207621 SV_141 C . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=62;END=11207683;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr19 11196136 severus_DUP3242 N 60 PASS PRECISE;SVTYPE=DUP;SVLEN=22820;END=11218956;STRANDS=-+;DETAILED_TYPE=tandem_duplication;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:378:0.26:0,0,1:42:15 - -2025-01-06 03:04:06,606 [DEBUG] Made mat -> True 33.86243386243386 -> - chr19 11207621 SV_141 C . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=62;END=11207683;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr19 11207621 severus_INV3243 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=62;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:247:0.39:0,0,1:30:19 - -2025-01-06 03:04:06,606 [DEBUG] chr19 11207621 SV_141 C . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=62;END=11207683;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr19 11208275 severus_INV3244 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=9528;STRANDS=--;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:365:0.28:0,0,1:41:16 - are not within REFDIST -2025-01-06 03:04:06,606 [DEBUG] chr19 11207621 SV_141 C . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=62;END=11207683;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr19 11208275 severus_INV3244 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=9528;STRANDS=--;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:365:0.28:0,0,1:41:16 - size similarity is too low (0.007) -2025-01-06 03:04:06,607 [DEBUG] Made mat -> False 0.2169045619927232 -> - chr19 11207621 SV_141 C . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=62;END=11207683;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr19 11208275 severus_INV3244 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=9528;STRANDS=--;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:365:0.28:0,0,1:41:16 - -2025-01-06 03:04:06,607 [DEBUG] chr19 11207681 SV_142 N . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=12043;END=11219724;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr19 11196136 severus_DUP3242 N 60 PASS PRECISE;SVTYPE=DUP;SVLEN=22820;END=11218956;STRANDS=-+;DETAILED_TYPE=tandem_duplication;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:378:0.26:0,0,1:42:15 - are not the same SVTYPE -2025-01-06 03:04:06,608 [DEBUG] chr19 11207681 SV_142 N . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=12043;END=11219724;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr19 11196136 severus_DUP3242 N 60 PASS PRECISE;SVTYPE=DUP;SVLEN=22820;END=11218956;STRANDS=-+;DETAILED_TYPE=tandem_duplication;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:378:0.26:0,0,1:42:15 - size similarity is too low (0.528) -2025-01-06 03:04:06,608 [DEBUG] Made mat -> False 34.06150437291032 -> - chr19 11207681 SV_142 N . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=12043;END=11219724;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr19 11196136 severus_DUP3242 N 60 PASS PRECISE;SVTYPE=DUP;SVLEN=22820;END=11218956;STRANDS=-+;DETAILED_TYPE=tandem_duplication;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:378:0.26:0,0,1:42:15 - -2025-01-06 03:04:06,608 [DEBUG] chr19 11207681 SV_142 N . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=12043;END=11219724;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr19 11207621 severus_INV3243 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=62;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:247:0.39:0,0,1:30:19 - size similarity is too low (0.005) -2025-01-06 03:04:06,609 [DEBUG] Made mat -> False 0.17160729607794292 -> - chr19 11207681 SV_142 N . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=12043;END=11219724;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr19 11207621 severus_INV3243 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=62;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:247:0.39:0,0,1:30:19 - -2025-01-06 03:04:06,609 [DEBUG] Made mat -> True 26.37493403352184 -> - chr19 11207681 SV_142 N . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=12043;END=11219724;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr19 11208275 severus_INV3244 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=9528;STRANDS=--;MAPQ=60;PHASESETID=10550509;HP=2;CLUSTERID=severus_3 GT:GQ:VAF:hVAF:DR:DV 0/1:365:0.28:0,0,1:41:16 - -2025-01-06 03:04:06,610 [DEBUG] Comparing chunk 78 -2025-01-06 03:04:06,611 [DEBUG] All FP -> False None -> - None chr19 29439310 severus_DEL3297 N 60 PASS IMPRECISE;SVTYPE=DEL;SVLEN=104;END=29439414;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=28716466;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:383:0.11:0,1,0:34:4 - -2025-01-06 03:04:06,611 [DEBUG] Comparing chunk 79 -2025-01-06 03:04:06,612 [DEBUG] All FN -> False None -> - chr19 38022545 SV_143 N N]chr20:28640515] . COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - None -2025-01-06 03:04:06,613 [DEBUG] Comparing chunk 80 -2025-01-06 03:04:06,613 [DEBUG] All FN -> False None -> - chr19 38981212 SV_144 G . COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=2314;END=38983526;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=3;CIEND1=-3;CIEND2=0;HOMLEN=3;HOMSEQ=TCA GT:PSL:PSO 0/1:.:. - None -2025-01-06 03:04:06,614 [DEBUG] Comparing chunk 81 -2025-01-06 03:04:06,614 [DEBUG] Made mat -> True 33.26744272446536 -> - chr19 44991106 SV_148 G . COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=1518;END=44992624;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=2;CIEND1=-2;CIEND2=0;HOMLEN=2;HOMSEQ=GA GT:PSL:PSO 0/1:.:. - chr19 44991108 severus_INV3345 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=1514;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=44817129;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:654:0.28:0,1,0:76:29 - -2025-01-06 03:04:06,616 [DEBUG] Comparing chunk 82 -2025-01-06 03:04:06,616 [DEBUG] Made mat -> True 66.66666666666666 -> - chr19 53132028 SV_149 T . COMPLEX SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=44818;END=53176846;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr19 53132028 severus_DUP3384 N 60 PASS PRECISE;SVTYPE=DUP;SVLEN=44818;END=53176846;STRANDS=-+;DETAILED_TYPE=tandem_duplication;MAPQ=60;PHASESETID=53078799;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:565:0.35:0,0,1:94:50 - -2025-01-06 03:04:06,617 [DEBUG] chr19 53132028 SV_149 T . COMPLEX SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=44818;END=53176846;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr19 53167794 severus_DEL3385 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=1392;END=53169186;STRANDS=+-;MAPQ=60;PHASESETID=53078799;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:818:0.19:0,0,1:132:30 - are not the same SVTYPE -2025-01-06 03:04:06,617 [DEBUG] chr19 53132028 SV_149 T . COMPLEX SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=44818;END=53176846;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr19 53167794 severus_DEL3385 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=1392;END=53169186;STRANDS=+-;MAPQ=60;PHASESETID=53078799;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:818:0.19:0,0,1:132:30 - size similarity is too low (0.031) -2025-01-06 03:04:06,617 [DEBUG] Made mat -> False 2.071317267936611 -> - chr19 53132028 SV_149 T . COMPLEX SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=44818;END=53176846;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr19 53167794 severus_DEL3385 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=1392;END=53169186;STRANDS=+-;MAPQ=60;PHASESETID=53078799;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:818:0.19:0,0,1:132:30 - -2025-01-06 03:04:06,618 [DEBUG] chr19 53167789 SV_150 G . SUBCLONAL-COMPLEX SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-1401;END=53169190;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr19 53132028 severus_DUP3384 N 60 PASS PRECISE;SVTYPE=DUP;SVLEN=44818;END=53176846;STRANDS=-+;DETAILED_TYPE=tandem_duplication;MAPQ=60;PHASESETID=53078799;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:565:0.35:0,0,1:94:50 - are not the same SVTYPE -2025-01-06 03:04:06,619 [DEBUG] chr19 53167789 SV_150 G . SUBCLONAL-COMPLEX SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-1401;END=53169190;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr19 53132028 severus_DUP3384 N 60 PASS PRECISE;SVTYPE=DUP;SVLEN=44818;END=53176846;STRANDS=-+;DETAILED_TYPE=tandem_duplication;MAPQ=60;PHASESETID=53078799;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:565:0.35:0,0,1:94:50 - size similarity is too low (0.031) -2025-01-06 03:04:06,619 [DEBUG] Made mat -> False 2.0847045968314797 -> - chr19 53167789 SV_150 G . SUBCLONAL-COMPLEX SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-1401;END=53169190;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr19 53132028 severus_DUP3384 N 60 PASS PRECISE;SVTYPE=DUP;SVLEN=44818;END=53176846;STRANDS=-+;DETAILED_TYPE=tandem_duplication;MAPQ=60;PHASESETID=53078799;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:565:0.35:0,0,1:94:50 - -2025-01-06 03:04:06,620 [DEBUG] Made mat -> True 66.23855387582336 -> - chr19 53167789 SV_150 G . SUBCLONAL-COMPLEX SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-1401;END=53169190;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr19 53167794 severus_DEL3385 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=1392;END=53169186;STRANDS=+-;MAPQ=60;PHASESETID=53078799;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:818:0.19:0,0,1:132:30 - -2025-01-06 03:04:06,621 [DEBUG] Comparing chunk 83 -2025-01-06 03:04:06,621 [DEBUG] All FP -> False None -> - None chr19 53185930 severus_BND3387_1 N [chr3:138126527[N 37.5 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND3387_2;STRANDS=--;MAPQ=37;CLUSTERID=severus_2 GT:GQ:VAF:hVAF:DR:DV 0/0:946:0.13:1,0,0:90:14 - -2025-01-06 03:04:06,622 [DEBUG] Comparing chunk 84 -2025-01-06 03:04:06,623 [DEBUG] All FP -> False None -> - None chr19 55068021 severus_DEL3403 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=434;END=55068455;STRANDS=+-;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/0:370:0.15:1,0,0:35:6 - -2025-01-06 03:04:06,623 [DEBUG] All FP -> False None -> - None chr19 55068125 severus_DEL3404 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=330;END=55068455;STRANDS=+-;INSLEN=327;INSSEQ=None;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/0:332:0.14:1,0,0:31:5 - -2025-01-06 03:04:06,623 [DEBUG] Comparing chunk 85 -2025-01-06 03:04:06,624 [DEBUG] All FP -> False None -> - None chr2 9737600 severus_INS13463 N CCTAGTGCTGTACTCCCTCTAGTCCTCCCGCTCCCTCTAGTACCCCCCCTCCCCCTAGTGCCCCCCACTCCCTCTAGTACCCCCCACTCCTCCTAGTACCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCACTCCTCCTAGTACCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCACTCCTCCTAGTACTCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCACTCCTAGTACCCCACTCCTCCTAGTACCCCATCCTCCTAGTACCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCCCTAGTACCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACCTCCTCCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTCAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCTCCTCCTCAGTACCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCCACTTCCTCCTAGTACCCCTCCTCCTAGTACCCACTCCTCCTAGTACCCCCCTCCTCCTAGTACCCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCCCTCCTCCTAGTACCCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCCACTCCCTCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCCACTCCCTCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCCACTCCCTCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCCACTCCCTCTAGTACCCCCACTCCTCCTAGTACCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCCACTCCCTCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCTCCTCCTAGTACCCCCACTCCTCCTAGTACCCCCACTCTCCTAGTACCCCCACTCCTCCTAGTACCCCACTCCTCCTAGTACCCCCTCCT 60 PASS PRECISE;SVTYPE=INS;SVLEN=8195;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=9312779;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:741:0.1:0,1,0:65:7 - -2025-01-06 03:04:06,625 [DEBUG] Comparing chunk 86 -2025-01-06 03:04:06,626 [DEBUG] Made mat -> True 65.9217644610903 -> - chr2 39789308 SV_6 AGTGGGTTACTGGCCTGTTTACACAGAGGATGGGAAGAAAGGCTTGGGCTTAATAACTCAAAGCTTTTTTAAGCCTTCTAAGTTCCAAG A . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-88;END=39789396;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=2;CIEND1=.;CIEND2=.;HOMLEN=2;HOMSEQ=GT GT:PSL:PSO 0/1:.:. - chr2 39789308 severus_DEL3594 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=89;END=39789397;STRANDS=+-;MAPQ=60;PHASESETID=39772864;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:603:0.32:0,1,0:119:55 - -2025-01-06 03:04:06,626 [DEBUG] Comparing chunk 87 -2025-01-06 03:04:06,627 [DEBUG] All FP -> False None -> - None chr2 80358805 severus_BND3661_1 N N]chr1:122627336] 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND3661_2;STRANDS=++;INSLEN=92;INSSEQ=None;MAPQ=60;CLUSTERID=severus_4 GT:GQ:VAF:hVAF:DR:DV 0/1:209:0.5:1,0,0:29:29 - -2025-01-06 03:04:06,627 [DEBUG] Comparing chunk 88 -2025-01-06 03:04:06,627 [DEBUG] Made mat -> True 33.45238095238095 -> - chr2 80401504 SV_8 C . COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=279;END=80401783;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr2 80401504 severus_INV3662 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=279;STRANDS=--;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=79328637;HP=1;CLUSTERID=severus_4 GT:GQ:VAF:hVAF:DR:DV 0/1:552:0.35:0,1,0:85:46 - -2025-01-06 03:04:06,628 [DEBUG] Comparing chunk 89 -2025-01-06 03:04:06,629 [DEBUG] Made mat -> True 97.0 -> - chr2 82711539 SV_9 G G]chr20:38430138] . COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=3;CIEND1=.;CIEND2=.;HOMLEN=3;HOMSEQ=CAC GT:PSL:PSO 0/1:.:. - chr2 82711542 severus_BND4166_2 N N]chr20:38430135] 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND4166_1;STRANDS=++;DETAILED_TYPE=inv_tra;MAPQ=60;PHASESETID=38406571|82597857;HP=1;CLUSTERID=severus_8 GT:GQ:VAF:hVAF:DR:DV 0/1:667:0.27:1,0,0:135:49 - -2025-01-06 03:04:06,630 [DEBUG] Comparing chunk 90 -2025-01-06 03:04:06,630 [DEBUG] Made mat -> True 99.0 -> - chr2 89324416 SV_10 N ]chrX:8495892]N . SUBCLONAL-COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr2 89324414 severus_BND7781_2 N ]chrX:8495892]N 55.5 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND7781_1;STRANDS=-+;MAPQ=55;PHASESETID=8341569|89204393;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:641:0.29:0,0,1:74:30 - -2025-01-06 03:04:06,631 [DEBUG] Comparing chunk 91 -2025-01-06 03:04:06,631 [DEBUG] All FP -> False None -> - None chr2 138335018 severus_DEL3794 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=55;END=138335073;STRANDS=+-;MAPQ=60;PHASESETID=138049422;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:1125:0.06:0,0,1:104:7 - -2025-01-06 03:04:06,631 [DEBUG] Comparing chunk 92 -2025-01-06 03:04:06,632 [DEBUG] Made mat -> True 66.20530012771391 -> - chr2 148633969 SV_12 AGAAAAAAGGAACCAATGAGATGAAGCTGTGTAAAATATTCTGATGAAGAATCACCTGGTATATTTGTTAAATGTATATTTCTGGGCCACATTCCAGATCAGCCAAATTGGAGTCTATGGGAGTAGCATCATTTAAAAATAAAT A . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-143;END=148634112;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=5;CIEND1=.;CIEND2=.;HOMLEN=5;HOMSEQ=GAAAA GT:PSL:PSO 0/1:.:. - chr2 148633969 severus_DEL3811 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=144;END=148634113;STRANDS=+-;MAPQ=60;PHASESETID=148534112;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:501:0.39:0,0,1:97:63 - -2025-01-06 03:04:06,633 [DEBUG] Comparing chunk 93 -2025-01-06 03:04:06,634 [DEBUG] Made mat -> True 66.66666666666666 -> - chr2 157838734 SV_13 C CTCTCCTCTGCTTGCTGCATGGCTCTTCCAAGTATGTACATCTGGGGAGAACGCACAACCCCATTTCTACTTCATGTTTAAACCTGCCTCATAAGG . SUBCLONAL-COMPLEX SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=95;SUBCLONAL=y;COMPLEX=u;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr2 157838734 severus_INS13891 N TCTCCTCTGCTTGCTGCATGGCTCTTCCAAGTATGTACATCTGGGGAGAACGCACAACCCCATTTCTACTTCATGTTTAAACCTGCCTCATAAGG 60 PASS PRECISE;SVTYPE=INS;SVLEN=95;MAPQ=60;PHASESETID=157796221;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:997:0.09:0,1,0:86:8 - -2025-01-06 03:04:06,635 [DEBUG] Comparing chunk 94 -2025-01-06 03:04:06,635 [DEBUG] All FP -> False None -> - None chr2 157917147 severus_INS13892 N 60 PASS PRECISE;SVTYPE=INS;SVLEN=184;INSIDE_VNTR=TRUE;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/0:895:0.08:1,0,0:77:7 - -2025-01-06 03:04:06,636 [DEBUG] Comparing chunk 95 -2025-01-06 03:04:06,637 [DEBUG] Made mat -> True 65.80641580641581 -> - chr2 219159513 SV_16 TTATATATATATGCATATATATATGCATATATATATATGCATATATATATGCATATATATATGCATATATATATGCA T . SUBCLONAL SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-76;END=219159589;SUBCLONAL=u;COMPLEX=n;CIPOS1=0;CIPOS2=22;CIEND1=.;CIEND2=.;HOMLEN=22;HOMSEQ=TATATATATATGCATATATATA GT:PSL:PSO 0/1:.:. - chr2 219159513 severus_DEL3964 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=77;END=219159590;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=217961235;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:641:0.29:0,1,0:77:31 - -2025-01-06 03:04:06,637 [DEBUG] Comparing chunk 96 -2025-01-06 03:04:06,638 [DEBUG] All FP -> False None -> - None chr2 238119362 severus_DEL4031 N 60 PASS IMPRECISE;SVTYPE=DEL;SVLEN=55;END=238119417;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=237897787;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:473:0.12:0,0,1:43:6 - -2025-01-06 03:04:06,639 [DEBUG] Comparing chunk 97 -2025-01-06 03:04:06,639 [DEBUG] Made mat -> True 62.641274799005146 -> - chr2 239599318 SV_17 TC TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAGATATTAAAGTCTTTATTTGCCCCCCCCCCATTTTTATTTTCAGTAATACAGGGTAAAATGAGTAGGATTACTTGATCTGGCCATCTATGGCCATTTTATGGAATGACAAACTAAGTTCAATACTGATAGAGTTGTATTCTGTGTATACATATAATAGAGTATATACTGTGTGTATAAAAAATTCAAGCATATGGAAAAACTTATTTAATCCAGTAATAAACCTTTATATTTTCTCATCAGTTTAATAATAACATTTTTTGCCAGTAATTGGGTATA . SUBCLONAL SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=339;END=239599319;SUBCLONAL=u;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr2 239599317 severus_INS14139 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTAAAGATATTAAAGTCTTTATTTGCCCCCCCCCCATTTTTATTTTCAGTAATACAGGGTAAAATGAGTAGGATTACTTGATCTGGCCATCTATGGCCATTTTATGGAATGACAAACTAAGTTCAATACTGATAGAGTTGTATTCTGTGTATACATATAATAGAGTATATACTGTGTGTATAAAAAATTCAAGCATATGGAAAAACTTATTTAATCCAGTAATAAACCTTTATATTTTCTCATCAGTTTAATAATAACATTTTTTGCCAGTAATTGGGTA 60 PASS PRECISE;SVTYPE=INS;SVLEN=319;MAPQ=60;PHASESETID=239458541;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:780:0.14:0,1,0:73:12 - -2025-01-06 03:04:06,640 [DEBUG] Comparing chunk 98 -2025-01-06 03:04:06,640 [DEBUG] All FP -> False None -> - None chr2 242182788 severus_BND4589_2 N N]chr3:11522] 48 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND4589_1;STRANDS=++;MAPQ=48 GT:GQ:VAF:hVAF:DR:DV 0/0:1125:0.07:1,0,0:124:9 - -2025-01-06 03:04:06,641 [DEBUG] Comparing chunk 99 -2025-01-06 03:04:06,641 [DEBUG] All FP -> False None -> - None chr20 16410056 severus_INS14283 N ATATATATGTTGGTACATATATATATGTAGGTACATATACATATATGTAGGTAC 60 PASS PRECISE;SVTYPE=INS;SVLEN=54;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=16035097;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:690:0.05:0,0,1:57:3 - -2025-01-06 03:04:06,641 [DEBUG] Comparing chunk 100 -2025-01-06 03:04:06,642 [DEBUG] Made mat -> True 66.66666666666666 -> - chr20 21980692 SV_151 A . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-44392;END=22025084;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=1;CIEND1=0;CIEND2=1;HOMLEN=1;HOMSEQ=T GT:PSL:PSO 0/1:.:. - chr20 21980692 severus_DEL4117 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=44392;END=22025084;STRANDS=+-;MAPQ=60;PHASESETID=21754120;HP=2 GT:GQ:VAF:hVAF:DR:DV 1/1:447:0.79:0,0,1:13:48 - -2025-01-06 03:04:06,643 [DEBUG] Comparing chunk 101 -2025-01-06 03:04:06,643 [DEBUG] All FP -> False None -> - None chr20 25499118 severus_BND2983_2 N [chr18:21493610[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2983_1;STRANDS=--;MAPQ=60;PHASESETID=20911267|25143452;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:411:0.46:0,1,0:58:50 - -2025-01-06 03:04:06,644 [DEBUG] Comparing chunk 102 -2025-01-06 03:04:06,644 [DEBUG] All FP -> False None -> - None chr20 38428242 severus_INV4165 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=1362;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;PHASESETID=38406571;HP=2;CLUSTERID=severus_8 GT:GQ:VAF:hVAF:DR:DV 0/1:654:0.27:0,0,1:132:50 - -2025-01-06 03:04:06,644 [DEBUG] All FN -> False None -> - chr20 38428244 SV_152 T [chr20:38429604[T . COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=n;COMPLEX=u;CIPOS1=0;CIPOS2=3;CIEND1=-3;CIEND2=0;HOMLEN=3;HOMSEQ=CTC GT:PSL:PSO 0/1:.:. - None -2025-01-06 03:04:06,645 [DEBUG] Comparing chunk 103 -2025-01-06 03:04:06,645 [DEBUG] All FP -> False None -> - None chr20 38430135 severus_BND4166_1 N N]chr2:82711542] 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND4166_2;STRANDS=++;DETAILED_TYPE=inv_tra;MAPQ=60;CLUSTERID=severus_8 GT:GQ:VAF:hVAF:DR:DV 0/1:667:0.27:1,0,0:135:49 - -2025-01-06 03:04:06,646 [DEBUG] Comparing chunk 104 -2025-01-06 03:04:06,646 [DEBUG] Made mat -> True 65.96856725146199 -> - chr20 40907684 SV_153 C . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-94;END=40907778;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr20 40907684 severus_DEL4170 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=95;END=40907779;STRANDS=+-;MAPQ=60;PHASESETID=40545267;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:667:0.26:0,1,0:173:61 - -2025-01-06 03:04:06,648 [DEBUG] Comparing chunk 105 -2025-01-06 03:04:06,648 [DEBUG] Made mat -> True 66.61798709342604 -> - chr20 51796494 SV_155 T . SUBCLONAL SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-1368;END=51797862;SUBCLONAL=y;COMPLEX=n;CIPOS1=0;CIPOS2=2;CIEND1=0;CIEND2=2;HOMLEN=2;HOMSEQ=GT GT:PSL:PSO 0/1:.:. - chr20 51796494 severus_DEL4191 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=1369;END=51797863;STRANDS=+-;MAPQ=60;PHASESETID=51718814;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:767:0.21:0,1,0:140:37 - -2025-01-06 03:04:06,649 [DEBUG] Comparing chunk 106 -2025-01-06 03:04:06,649 [DEBUG] All FP -> False None -> - None chr20 62257545 severus_BND4242_1 N N[chr20:62378069[ 60 PASS PRECISE;SVTYPE=BND;SVLEN=120524;MATE_ID=severus_BND4242_2;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=61618645;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:895:0.15:0,1,0:133:24 - -2025-01-06 03:04:06,650 [DEBUG] Comparing chunk 107 -2025-01-06 03:04:06,650 [DEBUG] All FP -> False None -> - None chr20 62378069 severus_BND4242_2 N ]chr20:62257545]N 60 PASS PRECISE;SVTYPE=BND;SVLEN=120524;MATE_ID=severus_BND4242_1;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=61618645;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:895:0.15:0,1,0:133:24 - -2025-01-06 03:04:06,651 [DEBUG] Comparing chunk 108 -2025-01-06 03:04:06,651 [DEBUG] All FP -> False None -> - None chr20 62755279 severus_INS14528 N ATCCTTCTCTCCCTCCTTCCTCCATTCACTCCTCTACCTCTCCTCCATCCATCCCTCTCTCCCTCCTTCCCTCCATTCATTCCTCTACCTCTCCCTCCCTTCCTTCCTCCTCCCTCCATCATCCCTCCCTCCCTCCATCCCTCATTCCATCCCTCCCTCCCTCCCTCCATCCCTCCCTTCATCTATCCTCCCTCCCTCCCTCCCTCCATCCCTCATTCCATCCCTCCCTCTC 60 PASS IMPRECISE;SVTYPE=INS;SVLEN=241;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=62744554;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:869:0.07:0,0,1:74:6 - -2025-01-06 03:04:06,652 [DEBUG] Comparing chunk 109 -2025-01-06 03:04:06,652 [DEBUG] All FP -> False None -> - None chr20 63443044 severus_INS14556 N CACCACCACCACCACCATCACCATCACCACCATCACCACCATCACCATCACCACCACCACCACCATCACCACCATCACCATCACCATCACCATCACCACCACCACCATCACCATTACCACCACCATTACCACCACCATCACCATCACCATCACCACCACCACCACCACCATCACCATCACCCACCATCACCATTATCACCACCACCATCACCACCATCACCACCACCACCATCACCATCACCACCACCATCACCATTATCACCATCACCATCACCACCATCACCATCACCATCACCACCACCACCATCACCACCACCACCATGATCACCACCATCACCATCACCACCATCACATCACCATCACCACCATCATCACCACCATCACCATCACCATCATCACCACCACCATCACCATTATCACCACCACCACCATCACCATCACCACCATCACCACCACCACCACCAT 60 PASS IMPRECISE;SVTYPE=INS;SVLEN=465;INSIDE_VNTR=TRUE;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/0:882:0.13:0,1,1:81:12 - -2025-01-06 03:04:06,652 [DEBUG] Comparing chunk 110 -2025-01-06 03:04:06,653 [DEBUG] Made mat -> True 66.45800679205851 -> - chr21 20917525 SV_157 TTCAAAAAAAAAATATCTTTCAAAACAACAAATACACCCTTTGACTCAGGCAAAACCCATTGGGGAGTGTATAGTTAAATTATACTTACAGTTTTGAAAGGATACATGAGCATATCAACAGAAGTAAAGACAGAGTAGAAGGGATATAGGAATAAACTGCATGTAACTACAGAAAAGACAGGGAAATAATGAGGAAATCAGAAAAAATAAGCTCCAAAATATTGCTAAAGGAAAATGGAAGGATAATGACTATTGTATATAGTATGCTTTTTTATATAAAAATACAAATATATGTATCTATGTACCCATCATCCATCCA T . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-318;END=20917843;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=2;CIEND1=.;CIEND2=.;HOMLEN=2;HOMSEQ=TC GT:PSL:PSO 0/1:.:. - chr21 20917525 severus_DEL4310 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=319;END=20917844;STRANDS=+-;MAPQ=60;PHASESETID=20586810;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:473:0.19:0,0,1:48:11 - -2025-01-06 03:04:06,654 [DEBUG] Comparing chunk 111 -2025-01-06 03:04:06,654 [DEBUG] All FP -> False None -> - None chr22 31903293 severus_INS14914 N CCCTACGTTCACACTCACACCCTCCCACCTTCACCCTACCAACCCCCACCTTCCACACCTATTCCTCAACCTTCCATACCTAAACCCCCCCCACCTTCTGGCACCTAAACCCCGCTACCTTCCACACCTAAACTCCCACCTTCGTAACCTTCCACATCTAAATCCCCACCTTCCACACTAACCCCCATCTTCTGTACCTCCACCTTCCACACCTATACCTTCTATACCACCTTCTATACCT 60 PASS PRECISE;SVTYPE=INS;SVLEN=241;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=31441550;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:639:0.05:0,0,1:53:3 - -2025-01-06 03:04:06,655 [DEBUG] Comparing chunk 112 -2025-01-06 03:04:06,655 [DEBUG] All FP -> False None -> - None chr22 45328230 severus_INS15007 N TGGGCTGGGGGTACGGGAGGCCTTTGGCCGGCGGCAGAACAAGCCCATGGAGTCTCTGGACTTGAAGGACAAGACCAAGGTG 60 PASS IMPRECISE;SVTYPE=INS;SVLEN=82;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=45044063;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:677:0.1:0,1,0:60:7 - -2025-01-06 03:04:06,656 [DEBUG] Comparing chunk 113 -2025-01-06 03:04:06,656 [DEBUG] All FP -> False None -> - None chr22 47732375 severus_DEL4539 N 60 PASS IMPRECISE;SVTYPE=DEL;SVLEN=91;END=47732466;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=47600623;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:741:0.06:0,0,1:62:4 - -2025-01-06 03:04:06,657 [DEBUG] Comparing chunk 114 -2025-01-06 03:04:06,657 [DEBUG] All FP -> False None -> - None chr22 49494358 severus_INS15074 N CTGGGCAGGGGTGTCCGGGGCCGTATGGAAGGGCTGGGCAGGGGTGTCCGGGGCCGTGTGGAAGAG 60 PASS PRECISE;SVTYPE=INS;SVLEN=66;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=49216990;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:537:0.1:0,1,0:47:5 - -2025-01-06 03:04:06,658 [DEBUG] Comparing chunk 115 -2025-01-06 03:04:06,658 [DEBUG] All FP -> False None -> - None chr3 11410 severus_BND4588_1 N N]chr11:135076382] 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND4588_2;STRANDS=++;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/1:256:0.29:1,0,0:29:12 - -2025-01-06 03:04:06,658 [DEBUG] All FP -> False None -> - None chr3 11522 severus_BND4589_1 N N]chr2:242182788] 48 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND4589_2;STRANDS=++;MAPQ=48 GT:GQ:VAF:hVAF:DR:DV 0/0:1125:0.07:1,0,0:124:9 - -2025-01-06 03:04:06,659 [DEBUG] Comparing chunk 116 -2025-01-06 03:04:06,659 [DEBUG] Made mat -> True 66.64577784689448 -> - chr3 101703348 SV_19 G . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-3190;END=101706538;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=5;CIEND1=0;CIEND2=5;HOMLEN=5;HOMSEQ=GAGAT GT:PSL:PSO 0/1:.:. - chr3 101703348 severus_DEL4787 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=3191;END=101706539;STRANDS=+-;MAPQ=60;PHASESETID=100800213;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:680:0.25:0,1,0:100:34 - -2025-01-06 03:04:06,660 [DEBUG] Comparing chunk 117 -2025-01-06 03:04:06,660 [DEBUG] All FP -> False None -> - None chr3 112164434 severus_INS15449 N GCTTCCTTCAGGAGCTCTTTTAGGGCAGGCCTGGTGGTGACAAAATCTCTCAGCATTTGCTTGTCTGTAAAGTATTTTATTTCTCCTTCACTTATGAAGCTTAGTTTGGCTGGATATGAAATTCTGGGTTGAAAATTCTTTTCTTTAAGAATGTTGAATATTGGCCCCCACTCTCTTCTGCCTTGTAGGGTTTCTGCCGAGAGATCCGCTGTTAGTCTGATGGGCTTCCCTTTGAGGGTAACCCGACCTTTCTCTCTGGCTGCCCTTAACATTTTTTCCTTCATTTCAACTTCGGTGAATCTGACAATTATGTGTCTTGGAGTTGCTCTTCTCGAGGAGTATCTTTGTGGTGTTCTCTGTATTTCCTGAATCTGAACGTTGGCCTGCCTTGCTAGATTGGGGAAGTTCTCCTGGATAATATTCTGCAGAGTGTTTTCCAACTTGGTTTCATTCTCCCCATCACTTTCAGGTACACCAATCAGACGTAGATTTGGTCTTTTCACATAGTCCCATATTTCTTGGAGGCTTTGCTCATTTCTTTTTATTCTTTTTTCTCTAAACTTCCCTTCTCGCTTCATTTCATTCATTTCATCTTCCGTCGCTGATACCCTTTCTTCCAGTTGATTGCATCGGCTCCTGAGGCTTCTGCATTCTTCACGTAGTTCTCGAGCCTTGGTTTTCAGCTCCATCAGCTCCTTTAAGCACTTCTCTATATTGGTTATTCTAGTTATACATTCTTCTAAGTTTTTTTCAAAGTTTTCAACTTCTTTGCCTTTGGTTTGAATGTCCTCCCATAGCTCAGAGTAATTTGATTGTCTGAAGCCTTCTACTCTCAGCTCGTCAAAGTCATTCTCCATCCAGCTTTGTTCCGTTGCTGGTGCGGAACTGCGTTCCTTTGGAGGAGGAGAGGCCCTCTGCTTTTTAGAGTTTCCAGTTTTTCTGTTCTGTTTTTTCCCCATGTTTGTGGTTTTATCTACTTTTGGTCTTTGATGATGGTGATGTACAGATGGGTTTTTGGTGTGGATGTCCTTTCTGTTTGTTAGTTTTCCTTCGAACAGACAGGACCCTCAGCTGCAGGTCTGTTGGAATACCCTGCCATGTGAGGTGTCAGTGTGCCCCTGTTGGGGGATGCCTCCCAGTTAGGCTGCTCGGGGGTCAGGGTCAGGCACTCACTTGAGGAGGCAGTCTGCCCCTTCTCAGATCTCCAGCTGCGTACTGGGAGAACCACTGCTTTCTTCAAAGCTGTCAGACAGGGACATTTAAGTCTGCAGAGGTTACTGCTGTCTTTTTGTTTGTCTGTGCCCTGCCCTCAGAGGTGGAGCCTACAGAGGCAGGCAGGCCTCCTTGAGCTGTGGTGGGCTCCACCCAGTTCGAGCTTCCCAGCTGCTTTGTTTACCTAAGCAAGCCTGGGCAATGGCGGGCGCCCCTCCCCCAGCCTCGCTGCCGCCTTGCAGTTTGATCACAGACTACTGTGCTAGCAATCAGCGAGACTCCATGGGCGTAGGACCCTCCGAGCCAGGTGCGGGATATAATCTCGTGGTATGCCGGTTTTTAAGCCCGTCGGAAAAGCGCAGTATTCGGGTGGGAGTGACCCAATTTTCCAGGTGCCGTCCGTCACCCCTTTCTCTGACTAGGAAAGGGAACTCCCTGACCCCTTGCACTTCCTGAGTGAGGCAATGCCTCGCCCTGCTTCGGCTCGCACACGGTGTGCGCACCCACTGACCTGTGCCCACTGTCTGGCACTCCCTAGTGAGATGAACCCGGTACCTCAGATGGAAATGCAGAAATCACCCGTCTTCTGCGTCGCTCATGCTGGGAGCTGTAGACTGGAGCTGTTCCGAATCTTGGCTCACAGCCCTCAATAAGTTATTTAAAACTAATACCAACTTAACTTTGACTGCAAAAAAGAGACAGAAGAAACAAACACACAAACAAAGACATCTGTACACATTAATTCCCAACTTACCCCACATTTTGATTTTTAATGTCACAACTTGCATTTTATATTGCTTATCTCTTTAAAATTGTTGTAGTTAGTATTATCTTAAATATTTTGTCTTTTGTTCTTCTTAGTAGGGATATAAGTGATTCACACACCATGATTACCATATTAGTGTAACAATCACATTGATATAATTTTCTTTCCATTTGAAGAATTTCCTTTAGCATTTCTTATAGGACAGGTCTGGTAGTGATAAATCCCCTCAAGTTTTTTTTTTGGTCTGGGAAAGTCCTTATTTCTCCTTTCTTTCTGAAGTTTAGCTTTTCTGAGTACAGTTTTCGTGCTTGGCAGATTTTTTTTTTTTCTTCAGCACTTTGAATATATCTTTCTACTCCTCCTGGCCTGTGAGGTTTCTGTTGAGAAGTCTGCTTTCAGGCATATTGGATTTCCCTTACATATTATTTCCTTCTATTTTTTCCTCATTGCTTTTGCTCAAAAGTCCCTTTTCCTTTCTTTATCTTTGGCTTTTGAGTACCTGATTATAATGTTTTGGGGTATTCTTATTTGAGTTAAATCTGATTGATGACTTAATCTTTTTGTATCTAGATATTTATCTCCTTGTCCAGGTTTGTAAAGATTTCTGTTATTTATTAAAACAAACTTTATACAACTCTTTCTTTCTCAGTTCCCTTTTTAACTTCAAAAACCAAAATATTTGTTCTTTTGATGTTGTCACCTAGACCTTGTAAGATATCTTTATTCTTTTTTTAATTCTTTTTCTCCTCTGACTCTATTTTCAAATGGACTGTCTTCAACTTCACTGATTCCTTCTTCTATTTTATCAATTCTGCTGTTGATGGTATTTCATTAATTTTATTTTTCAGCTTTAGGACTTCTGTTTGATTTTTAAAAATTTTGATTTCTGTTAAATTTCATTGATAAATTTCTGAATTCATTCTGTTTTCTTGAAGTTCAGAGAGTTTCCTTATAATGTTTTTTTGAATTCTTTGAGAGATCACACATCTCCATCACTTTAGGGTTGGTTTCTGACATCTTATTTTGTGCATTTGGTGAGGTCATATTTCTCTAAATATTCTTGATGCTTGTGGACATGTACATTGAGGGATTAGGTATTTATTTTAGTCTCCACAGTTTGCCTTTGCCTGTCCCTGTCTGTCTTTGGAGAGCCTTCCATGGATTCTGGCAGACTGATTGTTTAGTTACCTGAATCTGTGATCACTGCAGCCCTCTCAGCACTAGAGGATGCTCTAAGCCCAGGCTTACCAAGATTCTCACAAGGATTTCAAGGTTGATTTGGTTTTAAGGCCCAGATGGACCTGGGGAAGACCCAGGGAGGGTTCTGGGGTTGTGTGGGACTGCTGGTCTGGAATCTGAGTTCAGAAGACTGTCCCAATGGCCCAGATGGATGTGACTCTCTGCCCATCTCTGCATGGATATGTTGGGTCCCTGATTGCAGTGAGAGGAGTTGAAGTTGAGGCTGGGCCCCCTTGTGATCTGCCAGAGAAAGGAGGTTGATAGGCCTGTATTGTTGGCTTAGATGGGCATGCATCACCCAGCAGGTGCCTGCACAAACAAGGCAGTTCCTTGACTGTAGCTGGAGGAGCCAGAGCTGAGACTGTCCCCTCAGGATCTGCTGTGGAACAGAGGCTGGAGAGGTCAGTCTTGCTTCAGAGTAGTGCACATTACCCAGCACAGATAGGATAGCTCCCTGATGTAGTAGGAGGGGACAAAGTTGAGACAGAGCCCTCTGGGGATCGGCTGTGAGATGGAGGCTGGCATGCCTGTCACATCAGTTCAGATAGGTATGTGTTTCCCAGTAGGTCTCTGAACAGATGGGATAGTTCCCTGACTGCAGCAAGAAGGGCTGGAGCTCAGATTGGGTTGATTTGGGATCTGCTGTGGGACACAGACTGGAGAGTCTTGTCTTATTGCTTCAGAGGGGCATGCCTTGCAGGTTTCAGCACAGATGGGATAGTTTACTGGTTGCAGTGGGAGGAGCCAGACCTGAGACTTGGTGCCATCAGGATCTGCTGTGAGTTGGAGTTCGGCAAGCCTGTCAGGGAGGCTCAGACTCCCAGGTTGTGTGATATGGGTGATTCTCTCTCTGGATCCTTGTGTGAGCAGCTCTGAGCTGTGACCTCAGCTGAGAGTGGTTGAAGCTAAACCACAAGGAAACTTTCAGGTTCATCACTGAGATAGATGTTAGCAGGCAGATGAGTTTCTCTGCCAAGGCACAAGTATGCATGATACATCTTGGATCCCTTGACAGATGGTTTTGGTTGCAGGCTCAAGACCAAATGAGGAAGGAGCCAAGCCCCTTGGAGGACAGGACAATTTCAAGACTTGAATGTGGAAGCAAGCTTGTAGTATCAACTACCTGGAGTCAATCTGCTTCTCAAAATGATGCTCCTAGGTTGTGAGCTACGTGAAGACTTTACAAACTCCTATCTAAATTTTGAGGCTCCTGCAGAGAGGCTTTGGGCCATGTATGGGTACAGAATTTCTTTTTCGTGGGATATATGAATGGATTACCTTCTATTCCATTATCTTGGTTATGCCACTCTGTATATGCTTAATCTTAAGGTCAATGGGGACCCATACAATGGCAGTATTTTGTGTCCACATTGATGCAAAATTATATGATTGTACGTAATAAAGATTAAACTCATTTACGTTAGTAATATAATGTTATATTCTTGGTATTTTTACTTGATGTATATCACTGGTTTTTCTTTAACTTTTAGTTTAGGTTTGGGGGTACATGTGAAGAGTTTATTACATATGTAAACACGTTGTCACAGAAGTTTGTTGTGTATATTATTTCATCACCCAGGCATTAAGCCTAGTACCCAATAGTTATCTTTTCTGCTCCTCTCCTTCCTCTCATCCTCCTCCTTCAAGTAGACCCCAGTGTCTGCTATTTCTTTCCTTGCATCACTGGTTTTTCAAAAGTTATAATGTGGAAAATCAAGTTTTTAATGCTTACATAACATTCAATCACGTTGACTGATGTACTGATTTAGTTAACCATTCATTCATCATTATACATTTTTATTATTTCTTATGTTTCATTTTTAAAATATGCTCAATTATCATTTTCTTTTTTAGCTTTATATCTTTAGGATAAACATTTAGATATCATATTATTTAGTCAAAGGGTGTAAACACTTTTATGTCTTTTGGAATCTCCTGATAAATTTACTTTATTGTTTACATTGCTATTAGTAAAGTAAGAATATGTATCAAATTCACTACATTGCTTTTGGTTGAGAGGTATTATAATTCTTATAAAATTTCACAAATCAAATAGACCAAATACATAATTTGTTTCTGTAAACATTAACAACGTTGAACATTTTCCACATTGTGTTTTCTTTTTTTTTAATTATTATACTTTAAGTTTTAGGGTACATGTGCACAACGTGCAGGTTAGTTACATATGTATGCATGTGCCATGTTGGTGTGCTGCACCCAGTAACTCGTCATTTAACATTAGGCATATCTCCAAATGCTATTCCCTCCCCCCACACCCCACCCCACAACAGGCCCTGGTGTGTGATGTTCCCCTTTCTGTGTCCATGTGTTCTCACTGTTCAATTCCCACCTATGAGTGAGAACATGCAGTGTTTGGTTTTTTGTCCTTGCGATAGTTTGCTGAGAATGATGATTTCCAGCTTCATCCATGTCCCTACAAAGGACATGAACTCATCATTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTCCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCACAGTAAACATACGTGTGCATGTGTCTTTATAGAAGCATGATTTATAGTCCTTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGGTTGAACTAGTTTACAGTCCCACCAACAGTGTAAAAGTGTTCCTATTTCTCCACATCCTCTCCAGCACCTGTTGTTTCCTGACTTTTTAATGATCGCCATTCTAACTGGCTTGAGATGGTATCTCATTGTGGTGTTGATTTTCATTTCTCTGATGACCAGTGATGATGAGCATTTTTTCATGTATCTGTTGGCTGCATAAATGTCTTCTTTTGAGAAGTATCTGTTCATATCCTTTGCCCACTTTTTGATGGGGTTGTTTGTTTTTTTCTTGTAAATTTGTTTGAGTTCATTGTAGATTCTGGATATTAGCCCTTTGTCAGATGAGTAGATTGCAAAAATTTTCTCCCATTTTGTAGGTTGCCTGTTCACTCTGATGGTAGTTTCTTTTGCTGTGCAGAAGCTCTTTAGTTTAATTAGATCCCATTTGTCAATTTTGTCTTTTGTTGCCATTGCTTTTGGTGTTTTAGACATGAAGTCCTTGCCCATGCCTATGTCCTGAATGGTATTGCCTAGGTTTTCTTCTAGGGTTTGTATGGTTTTAGGCCTAACATTTAAGTCTTTAATCCATCTTGAATTAATTTTTGTATAAGATGTAAGGAAGGGATCCAGTTTCAGCTTTCTCCATATGGCTAGCCAGTTTTCCCAGCACCATTTGTTAAATAGGGAATCCTTTCCCCACTTCTTGTTTTTGTCAGGTTTGTCAAAGATCAGATAGTTGTAGATACGTGGCATTATTTCTGAGGGCTCTGTTCTGTTCCATTGGTCTATATCTCTGTTTTGGTACGAGTACCATGCTGTGTTGGTTACTGTAGCCATGTAGTATAGTTTGAAGTCAGGTAGCATGATGCCTCCAGCTTTGTTCTTTTGGCTTAGGATTGACTTGGCAATGTGGTACCTTTTATGGTTCCATATGAACTTTAAAGTAGTTTTTTCCAATTCTGTGAAGAAAGGCATTGGTAGCTTGGTGGGGATGACATTGAATCTATAAATTACCTTGGGCGGTATGGCCATTTTCATGATATTGATTCTTCCTACCCATGAGCATGGAATGTCCTTCCATTTGTTTGTATCCTCTTTCATTTCATTGAGCAGTGGTTTGTAGTTCTCCTTGAAGAGGTCCTTCACGTCCCTTGTAAGTTGGATTCCTAGGTACTTTATTCTCTTTGAAGCAATTGTGAATGGGAGTTCACTCATGATTTGGCTCTCTGTTTGTCTGTTGTTGGTGTATAAGAATGCTTGTGATTTTTGCACATTGATTTTGTATCCTGAGACTTTGCTGAAGTTGCCTATCAGCTTAAGGAGATTTTGGGCTGAGATGACGGGGTTTTCTAGATATACAGTCATGTCATCTGCAAACAGGGACAATTTGACTTCCTCTTTTCCTAATTGACTACCCTTTATTTCCTTCTCCTGCCTGATTGCCCTGGCCAGAACTTCCAACACTATGTTGAATAGGAATGGTGAGAGAGGGCATCCCTGTCTTGTGCCAGTTTTCAAAGGAATGCTTCCAGTTTTTGCCCATTCAGTATGATATTGGCTGTGGGTTTGTCGTAGATAGCTCTTATTATTTTGAAATACATCCCATCAATACCTAATTTTTTGAGAGTTTTTAGCATGAAGGGCTGTTTAATTTTTGTTGAAGGCCTTTTCTGCATCTATTGGGATAATCATATGGTTTTTGTCATTGTCTCTGTTTATATGCTGGATTTTGTTTATTGATTTGCATATGTTGAACCAGCCTTGCATCCCAGGGATGAAGCCCACTTGATCATGGCGGATAAGCTTTTTATTGTGCTGCTGGATTTGGTTTGCCAGTATTTTATTGAGGATTTTTGCATCTATGTTCATCAGGGATATTGGTCTAAAATTCTCTTTTTTGTTGTGTCTCTGCCATGCTTTGGTATTAGGATGATGCTGGCCTCATAAAATGAGTTAGGGGGGATTCCCTCTTTTTCTATTGATTGGAATAGTTTCAGAAGGAATGGTACCAGCTCCTCCTTGTACCTCTGGTAGAATTCGGCTGTGAATCCTTCTGGTCCTGGACTTTTTTTGGTTGGTAAGCTATTGATTATTGCCTCAATTTCAGAGCCTGTTATTGGTCTATTCAGAGATTCAACTTCTTGCTGGTTTAGTCTTGGGAGGGTGTATGTGTCGAGGAATTTATCCATTTCTTGTAGATTTTCTAGTTTATTTGCATAGAGTTGTTTACAGTATTCTCTGATGGTAGTTTGTATTTCTGTGGGATCTGTAGTGATATCCCCTTTATCATTTTTTATTGCATCTATTTGATTCTTCTGTCTTTTCTTCTTTATTTGTCTTGCTAGCAGTCTATCAATTTTGTTGATATTTTCAAAAAGCAGTGCCTGGATTCATTGAGTTTTTGGAGGATTTTTTGTGTCTCTATTTCCTTCAGTTCTGCTCTGATCTTAGTTATTTCTTGCCTTCTGCTAGCTTTTGAATGTGTTTGCTCTTGCTTCTGTATTTCTTTTAATTGTGATGTTAGGGTGTCAATTTTAGATCTTTCCTGCTTTCTCTTGTGGTCATTTAGTGCTATAAATTTCCCTCTACACACTGCTTTGAATGTGTCCCAGAGATTCTGGTATGTTGTGTCTTTGTTCTCATTGGTTTCAAAGAACATCTTTATTTCTGCCTTCATTTCGTTATGTACCCAGTAGTCATTCAGGAGCAGGTTGTTCAGTTTCCATGTAGTTGAGCGGTTCTGAGTGAGTTCCTTAATCCTGAGTTCTAGTTTGATTGCCCTGTGGTCCGAGAGATAGTTTGTTATAATTTCTGTTCTTTTACATTTGCTGAGGAGAGCTTTACTTCCAACTATGTGGTCAATTTTGGAATAAGTGTGGTGTGGTGCTGAGAAGAATGTATATTCTGTTGATTTGGGGTGCAGAGTTCTGTAGATGTGTATTAGGTCCACTTGGTGCACAGCTGAGTTCAATTCCTGGATATCCTTGTTAACTTTTTGTCTCATTGATCTGTCTAATGTTGGCAGTGGGGTGTTAAAGTCTCCCTTTATTATTGTGTGGGAGTCTAAGTCTCTTTGTAGGTCTCTAAGGACTTGCTTTATGAATCTGGGTGCTCCTGTATTGGGTGCATATATATTTAGGATAGTTAGCTCTTCTCGTTGAATTGATCCCTTTACCATTATGTAATGGCCGTCTTGTCTCTTTTGATCTTTGTTGGTTTAAAGTCTGTTTTATCAGAGACTAGGATTGCAACCCTGCCTTTCTTGTTTTCCATTTGCTTGGTAGATCTTCCTGCATCCCTTTATTTTGAGCCTATATATGTCTCTGCATGTGAGGTGGGTTTCCTGAATACAGCACACTGATGGGTCTTGACTCTTTATCCAATTTGCCAGTCTGTGTCTTTTAATTGGAGCATTTAGCCCATTTACATTTATAGTTAATATTGTTATGTGTGAATTTGATCCTGTCATTATGATGTTAGCTGTTCATTTTGCTCATTAGTTGATGCAGTTTCTTCCTAGCTTCAATGATCTGTAGAATTTGGCATGTTTTTGCAGTGGCTGGTACTGATTGTTCCTTTCCATGTTTAGT 60 PASS PRECISE;SVTYPE=INS;SVLEN=9499;MAPQ=60;PHASESETID=112126747;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:1125:0.07:0,1,0:153:11 - -2025-01-06 03:04:06,662 [DEBUG] Comparing chunk 118 -2025-01-06 03:04:06,662 [DEBUG] All FP -> False None -> - None chr3 138126527 severus_BND3387_2 N [chr19:53185930[N 37.5 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND3387_1;STRANDS=--;MAPQ=37;PHASESETID=53078799|138122486;HP=1;CLUSTERID=severus_2 GT:GQ:VAF:hVAF:DR:DV 0/0:946:0.13:1,0,0:90:14 - -2025-01-06 03:04:06,663 [DEBUG] Comparing chunk 119 -2025-01-06 03:04:06,663 [DEBUG] Made mat -> True 100.0 -> - chr3 139976414 SV_20 C C]chr13:114353244] . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=1;CIEND1=.;CIEND2=.;HOMLEN=1;HOMSEQ=A;MATEID=SV_172;CLUSTERID=cluster_3 GT:PSL:PSO 1|0:chr13*114353244*1,.:1,. - chr3 139976414 severus_BND1960_2 N N]chr13:114353244] 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1960_1;STRANDS=++;MAPQ=60;PHASESETID=0|139256694;HP=1;CLUSTERID=severus_2 GT:GQ:VAF:hVAF:DR:DV 0/1:424:0.45:0,0,1:75:62 - -2025-01-06 03:04:06,664 [DEBUG] Comparing chunk 120 -2025-01-06 03:04:06,665 [DEBUG] All FN -> False None -> - chr3 139998694 SV_21 C [chr3:193903984[C . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_174;CLUSTERID=cluster_3 GT:PSL:PSO 1|0:chr13*114353244*1,.:3,. - None -2025-01-06 03:04:06,665 [DEBUG] Comparing chunk 121 -2025-01-06 03:04:06,666 [DEBUG] All FP -> False None -> - None chr3 184714600 severus_INV4962 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=2714;STRANDS=--;MAPQ=60;CLUSTERID=severus_5 GT:GQ:VAF:hVAF:DR:DV 0/1:358:0.51:1,0,0:47:49 - -2025-01-06 03:04:06,666 [DEBUG] All FN -> False None -> - chr3 184714592 SV_23 T T]chr3:184716953] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=1;CIEND1=-1;CIEND2=0;HOMLEN=1;HOMSEQ=A;MATEID=SV_175;CLUSTERID=cluster_4 GT:PSL:PSO 0/1:.:. - None -2025-01-06 03:04:06,666 [DEBUG] All FN -> False None -> - chr3 184714601 SV_25 G [chr3:184717315[CAG . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_176;CLUSTERID=cluster_4 GT:PSL:PSO 0/1:.:. - None -2025-01-06 03:04:06,667 [DEBUG] Comparing chunk 122 -2025-01-06 03:04:06,667 [DEBUG] All FN -> False None -> - chr3 184716953 SV_175 T T]chr3:184714592] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=1;CIEND1=-1;CIEND2=0;HOMLEN=1;HOMSEQ=A;MATEID=SV_23;CLUSTERID=cluster_4 GT:PSL:PSO 0/1:.:. - None -2025-01-06 03:04:06,668 [DEBUG] All FN -> False None -> - chr3 184717315 SV_176 C [chr3:184714601[TGC . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_25;CLUSTERID=cluster_4 GT:PSL:PSO 0/1:.:. - None -2025-01-06 03:04:06,669 [DEBUG] Comparing chunk 123 -2025-01-06 03:04:06,669 [DEBUG] chr3 192188396 SV_27 C [chr11:68232231[C . PASS SVTYPE=BND;EVENTTYPE=TRA:BALANCED;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=2;CIEND1=.;CIEND2=.;HOMLEN=2;HOMSEQ=CC;MATEID=SV_90;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,2 - and chr3 192188390 severus_BND1186_2 N ]chr11:68233077]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1186_1;STRANDS=-+;MAPQ=60;PHASESETID=68002185|190937960;HP=1;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:455:0.69:0,1,0:23:52 - BND join POS not within BNDDIST -2025-01-06 03:04:06,670 [DEBUG] Made mat -> False None -> - chr3 192188396 SV_27 C [chr11:68232231[C . PASS SVTYPE=BND;EVENTTYPE=TRA:BALANCED;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=2;CIEND1=.;CIEND2=.;HOMLEN=2;HOMSEQ=CC;MATEID=SV_90;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,2 - chr3 192188390 severus_BND1186_2 N ]chr11:68233077]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1186_1;STRANDS=-+;MAPQ=60;PHASESETID=68002185|190937960;HP=1;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:455:0.69:0,1,0:23:52 - -2025-01-06 03:04:06,670 [DEBUG] Made mat -> True 99.0 -> - chr3 192188396 SV_27 C [chr11:68232231[C . PASS SVTYPE=BND;EVENTTYPE=TRA:BALANCED;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=2;CIEND1=.;CIEND2=.;HOMLEN=2;HOMSEQ=CC;MATEID=SV_90;CLUSTERID=cluster_1 GT:PSL:PSO 0|1:.,chr11*68232232*1:.,2 - chr3 192188394 severus_BND1184_2 N [chr11:68232231[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1184_1;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;PHASESETID=68002185|190937960;HP=1;CLUSTERID=severus_0 GT:GQ:VAF:hVAF:DR:DV 0/1:398:0.53:1,0,0:52:59 - -2025-01-06 03:04:06,671 [DEBUG] Comparing chunk 124 -2025-01-06 03:04:06,671 [DEBUG] All FN -> False None -> - chr3 193903984 SV_174 A [chr3:139998694[A . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_21;CLUSTERID=cluster_3 GT:PSL:PSO 1|0:chr13*114353244*1,.:3,. - None -2025-01-06 03:04:06,672 [DEBUG] Comparing chunk 125 -2025-01-06 03:04:06,672 [DEBUG] All FP -> False None -> - None chr4 1429358 severus_DEL5055 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=5241;END=1434599;STRANDS=+-;MAPQ=60;PHASESETID=990916;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:217:0.16:0,0,1:21:4 - -2025-01-06 03:04:06,672 [DEBUG] Comparing chunk 126 -2025-01-06 03:04:06,673 [DEBUG] All FP -> False None -> - None chr4 8631490 severus_DEL5101 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=5658;END=8637148;STRANDS=+-;MAPQ=60;PHASESETID=8074008;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:447:0.17:0,1,0:44:9 - -2025-01-06 03:04:06,673 [DEBUG] Comparing chunk 127 -2025-01-06 03:04:06,674 [DEBUG] Made mat -> True 66.50554949526432 -> - chr4 14331601 SV_28 T TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCTCACATATTCTTCTTTGTTTTATTTATAATTTTTTTTTTTTACAATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCACTGCACCCACTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGGTTTCCAATTTCATCCATGTCCCTACAAAGGATATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGGCATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCGCAATAAACATATGTGTGCATGTGTCTTTATAGCAGCATGATTTATACTCATTTGGGTATATACCCA . COMPLEX SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=620;END=14331601;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr4 14331601 severus_INS15849 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCCTCTCACATATTCTTCTTTGTTTTATTTATAATTTTTTTTTTTTACAATTCTTTTTTTTTTTTTTTTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCACTGCACCCACTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGGTTTCCAATTTCATCCATGTCCCTACAAAGGATATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGGCATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCGCAATAAACATATGTGTGCATGTGTCTTTATAGCAGCATGATTTATACTCATTTGGGTATATACCCA 60 PASS PRECISE;SVTYPE=INS;SVLEN=619;MAPQ=60;PHASESETID=14081825;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:281:0.5:0,0,1:39:39 - -2025-01-06 03:04:06,675 [DEBUG] Comparing chunk 128 -2025-01-06 03:04:06,675 [DEBUG] Made mat -> True 66.6319715476551 -> - chr4 57512446 SV_29 A . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-1920;END=57514366;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=5;CIEND1=0;CIEND2=5;HOMLEN=5;HOMSEQ=CTGTG GT:PSL:PSO 0/1:.:. - chr4 57512446 severus_DEL5194 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=1921;END=57514367;STRANDS=+-;MAPQ=60;PHASESETID=56437256;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:309:0.47:0,0,1:41:36 - -2025-01-06 03:04:06,676 [DEBUG] Comparing chunk 129 -2025-01-06 03:04:06,677 [DEBUG] Made mat -> True 66.58734354610644 -> - chr4 112897566 SV_30 T TTAAAACAGATAATCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCATTCAACAAATATTTATTAAACACCTTCTTTCTTTAAATTCCAAATTCCTCATTTGAAGCAGTCCAAATGCTCAGCTGTCCCAAGGCTGTTCTACTCTCCATACAAAGCTTTAGTTTCTCCAGCATATCCCCATTACCACATCTCATTTTCCATCCAGGATTCTTCCTATTTCCATATTTTTACTCATTTTGCCTGAAATGATCTTCCCTTTTTCCTCCACCAATTCAAATCTGAATCATTCTTCAAAGCCTAGCTGAAGTCACCCTCGCCCCCGGACCCTGGCCTAATTGCCTTCATGCCATTCTGTGTGACATTATAATATTGAGCTTAAGTTGCATTCCACACAAACACTTGATATTTCTTGATTTGAATAGTTCTATTTTTATTATTGTTAGTAGAGACAGGACCTTCCTCTGTTTGGAGTGCAGTGACACAACCATAGCTCACTGCAGCCTTAAACTCCTGGGCTCAAGGGGTCCTCCTTCTTCAGTCTCTCAAGTATCTAGTACTACAAATATATGCCACCACACCCAGATAATTTTTATTGTTTGTAGAGATAGGGTCTCACGGTATTGTTCAGGCTGGTCTCGAACTTCTGGCTTCAAGCAATCCTCTCATCTCAGCCTCCCAAAGCACTGAGACTATAGGCATCAGCCATCCCTCAGAAATAATGCCGCATATCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC . PASS SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=1259;END=112897566;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=18;CIEND1=0;CIEND2=18;HOMLEN=18;HOMSEQ=TAAAACAGATAATCTTTT GT:PSL:PSO 0/1:.:. - chr4 112897566 severus_INS16120 N TAAAACAGATAATCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCATTCAACAAATATTTATTAAACACCTTCTTTCTTTAAATTCCAAATTCCTCATTTGAAGCAGTCCAAATGCTCAGCTGTCCCAAGGCTGTTCTACTCTCCATACAAAGCTTTAGTTTCTCCAGCATATCCCCATTACCACATCTCATTTTCCATCCAGGATTCTTCCTATTTCCATATTTTTACTCATTTTGCCTGAAATGATCTTCCCTTTTTCCTCCACCAATTCAAATCTGAATCATTCTTCAAAGCCTAGCTGAAGTCACCCTCGCCCCCGGACCCTGGCCTAATTGCCTTCATGCCATTCTGTGTGACATTATAATATTGAGCTTAAGTTGCATTCCACACAAACACTTGATATTTCTTGATTTGAATAGTTCTATTTTTATTATTGTTAGTAGAGACAGGACCTTCCTCTGTTTGGAGTGCAGTGACACAACCATAGCTCACTGCAGCCTTAAACTCCTGGGCTCAAGGGGTCCTCCTTCTTCAGTCTCTCAAGTATCTAGTACTACAAATATATGCCACCACACCCAGATAATTTTTATTGTTTGTAGAGATAGGGTCTCACGGTATTGTTCAGGCTGGTCTCGAACTTCTGGCTTCAAGCAATCCTCTCATCTCAGCCTCCCAAAGCACTGAGACTATAGGCATCAGCCATCCCTCAGAAATAATGCCGCATATCTACAACTATCTGATCTTTGACAAACCTGAGAAAAACAAGCAATGGGGAAAGGATTCCCTATTTAATAAATGGTGCTGGGAAAACTGGCTAGCCATATGTAGAAAGCTGAAACTGGATCCCTTCCTTACACCTTATACAAAAATCAATTCAAGATGGATTAAAGATTTAAACGTTAAACCTAAAACCATAAAAACCCTAGAAGAAAACCTAGGCATTACCATTCAGGACATAGGCGTGGGCAAGGACTTCATGTCCAAAACACCAAAAGCAATGGCAACAAAAGACAAAATTGACAAATGGGATCTAATTAAACTAAAGAGCTTCTGCACAGCAAAGAAACTACCATCAGAGTGAACAGGCAACCTACAACATGGGAGAAAATTTTTGCAACCTACTCATCTGACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTC 60 PASS PRECISE;SVTYPE=INS;SVLEN=1260;ALINGED_POS=chr4:58753095-58754355;MAPQ=60;PHASESETID=112115958;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:411:0.46:0,1,0:68:59 - -2025-01-06 03:04:06,678 [DEBUG] Comparing chunk 130 -2025-01-06 03:04:06,679 [DEBUG] Made mat -> True 66.07799565968838 -> - chr4 134389657 SV_31 T TAAAAAAATTTAAAATTTTTGGTGGGGTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACACATTAGTGGGTGCAGTGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . PASS SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=226;END=134389657;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=19;CIEND1=.;CIEND2=.;HOMLEN=19;HOMSEQ=AAAAAAATTTAAAATTTTT GT:PSL:PSO 0/1:.:. - chr4 134389657 severus_INS16155 N AAAAAAATTTAAAATTTTTGGTGGGGTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACACATTAGTGGGTGCAGTGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 60 PASS PRECISE;SVTYPE=INS;SVLEN=224;MAPQ=60;PHASESETID=133835731;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:373:0.5:0,1,0:63:62 - -2025-01-06 03:04:06,680 [DEBUG] Comparing chunk 131 -2025-01-06 03:04:06,680 [DEBUG] Made mat -> True 66.61007357102434 -> - chr5 4450315 SV_34 T TGAAAGTAGGCATATCGTACACAAATTTGATGAGTTTTGACACATGCAAACAGCCATGAAACCATCATAACAATTAAAATAACAAACATTTCCATGTTTGCTTTGTTTTGTTTGTTTTTTTTTTTTTTTTCATGTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTTGTGCGCTGCACCCACTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTAAATTTGTGTACGTTAAATATGTGAAACTTATTGTATGCTGGTTACACCTCAATAAAGCTGTTAAATTTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAGATGTAAGTAGAAATAGCAAAAAGTTAAAAAGCAGGACAAATTAAAATAGAGTTTTTATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . COMPLEX SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=589;END=4450315;SUBCLONAL=n;COMPLEX=u;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr5 4450315 severus_INS16493 N GAAAGTAGGCATATCGTACACAAATTTGATGAGTTTTGACACATGCAAACAGCCATGAAACCATCATAACAATTAAAATAACAAACATTTCCATGTTTGCTTTGTTTTGTTTGTTTTTTTTTTTTTTTTCATGTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTTGTGCGCTGCACCCACTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCTCCCCCCTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTAAATTTGTGTACGTTAAATATGTGAAACTTATTGTATGCTGGTTACACCTCAATAAAGCTGTTAAATTTTTTTAAAAAAAAAAAAAAAAAAAAAAAAAAAGATGTAAGTAGAAATAGCAAAAAGTTAAAAAGCAGGACAAATTAAAATAGAGTTTTTATTAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 60 PASS PRECISE;SVTYPE=INS;SVLEN=588;MAPQ=60;PHASESETID=4186519;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:578:0.33:0,1,0:86:43 - -2025-01-06 03:04:06,681 [DEBUG] Comparing chunk 132 -2025-01-06 03:04:06,682 [DEBUG] All FN -> False None -> - chr5 20023770 SV_35 C C]chr5:155777977] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=2;CIEND1=-2;CIEND2=0;HOMLEN=2;HOMSEQ=CA;MATEID=SV_42;CLUSTERID=cluster_2 GT:PSL:PSO 0|1:.:. - None -2025-01-06 03:04:06,682 [DEBUG] All FN -> False None -> - chr5 20023782 SV_36 A [chr5:155777977[A . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=1;CIEND1=-1;CIEND2=0;HOMLEN=1;HOMSEQ=A;MATEID=SV_41;CLUSTERID=cluster_2 GT:PSL:PSO 0|1:.:. - None -2025-01-06 03:04:06,683 [DEBUG] Comparing chunk 133 -2025-01-06 03:04:06,683 [DEBUG] Made mat -> True 65.46536796536796 -> - chr5 22078163 SV_37 CATACTTTAACTTCATGTCTTCAGCAAAGAATGTCAAAAATTGAACGAAATATAT C . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-54;END=22078217;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=1;CIEND1=.;CIEND2=.;HOMLEN=1;HOMSEQ=A GT:PSL:PSO 0/1:.:. - chr5 22078163 severus_DEL5652 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=55;END=22078218;STRANDS=+-;MAPQ=60;PHASESETID=22023581;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:590:0.33:0,1,0:113:55 - -2025-01-06 03:04:06,684 [DEBUG] Comparing chunk 134 -2025-01-06 03:04:06,684 [DEBUG] All FP -> False None -> - None chr5 36023180 severus_BND5692_1 N N[chr5:39360025[ 60 PASS PRECISE;SVTYPE=BND;SVLEN=3336845;MATE_ID=severus_BND5692_2;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=35987449|39316484;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:629:0.29:0,0,1:118:49 - -2025-01-06 03:04:06,685 [DEBUG] Comparing chunk 135 -2025-01-06 03:04:06,685 [DEBUG] All FP -> False None -> - None chr5 39360025 severus_BND5692_2 N ]chr5:36023180]N 60 PASS PRECISE;SVTYPE=BND;SVLEN=3336845;MATE_ID=severus_BND5692_1;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=35987449|39316484;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:629:0.29:0,0,1:118:49 - -2025-01-06 03:04:06,685 [DEBUG] Comparing chunk 136 -2025-01-06 03:04:06,686 [DEBUG] Made mat -> True 100.0 -> - chr5 52747359 SV_171 T T]chr1:23272628] . PASS SVTYPE=BND;EVENTTYPE=TRA:UNBALANCED;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_1 GT:PSL:PSO 1|0:.:. - chr5 52747359 severus_BND164_2 N N]chr1:23272628] 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND164_1;STRANDS=++;MAPQ=60;PHASESETID=23220753|52503495;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:411:0.47:0,1,0:55:48 - -2025-01-06 03:04:06,686 [DEBUG] Comparing chunk 137 -2025-01-06 03:04:06,687 [DEBUG] All FP -> False None -> - None chr5 71009536 severus_DEL5752 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=5689;END=71015225;STRANDS=+-;MAPQ=60;PHASESETID=70931237;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:511:0.07:0,1,0:43:3 - -2025-01-06 03:04:06,688 [DEBUG] Comparing chunk 138 -2025-01-06 03:04:06,688 [DEBUG] Made mat -> True 65.8173753110462 -> - chr5 79179752 SV_39 CCTGTAATCCCAGCTACTCAGGAGGCTGAGGCAGGAGAATCGCTTGAACCTGGGAGGCGGAGGTTGCAGTGAGTCGAG C . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-77;END=79179829;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr5 79179752 severus_DEL5774 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=78;END=79179830;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=78798500;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:151:0.5:0,0,1:21:21 - -2025-01-06 03:04:06,689 [DEBUG] Comparing chunk 139 -2025-01-06 03:04:06,689 [DEBUG] All FN -> False None -> - chr5 155777977 SV_41 T [chr5:20023782[T . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=1;CIEND1=-1;CIEND2=0;HOMLEN=1;HOMSEQ=T;MATEID=SV_36;CLUSTERID=cluster_2 GT:PSL:PSO 0|1:.:. - None -2025-01-06 03:04:06,689 [DEBUG] All FN -> False None -> - chr5 155777977 SV_42 T T]chr5:20023770] . PASS SVTYPE=BND;EVENTTYPE=INV;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=2;CIEND1=-2;CIEND2=0;HOMLEN=2;HOMSEQ=TG;MATEID=SV_35;CLUSTERID=cluster_2 GT:PSL:PSO 0|1:.:. - None -2025-01-06 03:04:06,690 [DEBUG] Comparing chunk 140 -2025-01-06 03:04:06,690 [DEBUG] All FP -> False None -> - None chr5 172418419 severus_BND5954_1 N N[chr5:172626376[ 60 PASS PRECISE;SVTYPE=BND;SVLEN=207957;MATE_ID=severus_BND5954_2;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/1:462:0.59:1,0,0:52:74 - -2025-01-06 03:04:06,691 [DEBUG] Comparing chunk 141 -2025-01-06 03:04:06,691 [DEBUG] All FP -> False None -> - None chr5 172626376 severus_BND5954_2 N ]chr5:172418419]N 60 PASS PRECISE;SVTYPE=BND;SVLEN=207957;MATE_ID=severus_BND5954_1;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=171972316|172465449;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:462:0.59:1,0,0:52:74 - -2025-01-06 03:04:06,692 [DEBUG] Comparing chunk 142 -2025-01-06 03:04:06,692 [DEBUG] All FP -> False None -> - None chr5 176031047 severus_INS16942 N GGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGGGTGAGGGTGTGGGTGGGGATGTGAGGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGGGTGAGGGTGTGGGTGGGGATGTGAGGGTGGGGGTGTGTGGGGGAGGGTGTGGGTGGGGGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGTGGGGGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGATGTGAGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGGGTGGGGGTGTGGGCGAGGGTGTGGGTGGGGATGTGAGGGTGGGGGTGTGTGGGGGAGGGTGTGGGTGGGGGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGTGGGGGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGGGCGAGGGTGTGGGTGGGGATGTGAGGGTGGGGGTGTGTGGGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGGGAGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGTGGGGGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGTGGGGGAGGCTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGGGTGAGGGTGTGGGTGGGGATGTGAGGGTGGGGGTGTGTGGGGGAGGGTGTGGGTGGGGGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGGGTGGGGGTGTGTGGGGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGTGGGGGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGGGAGGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGTGGGGGAGGGTGTGGGTGGGGGTGTGTGGGGGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGTGGGGGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGGTGGGGGTGTGGGGTGGGGGGTGTGGGTGAGGGTGTGTGGGGGAGGGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGATGTGTGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGTGGGGGAGGGGGTGGGGTTGTGGGTGAGGGTGTGGGTGGGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGTGGGGGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGTGTGGGTGAGGGTGTGGGTGGGGATGTGAGGTGGGGGTGTGTGGGGGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGGGTGAGGGTGTGGGTGGGGTTGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGTGGGGGAGGGTGTGGGTGGGGGTGTGTGGGGGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGTGGGGGAGGGTGTGGGTGGGGGTGTGTGGGGAGGGTGTGGGTGGGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGGTGAGGGTGTGGGTGAGGGTGTGGGTGGGTGTGTGGGTGAGGGTGTGGGTGTGTGGGTGGGGGGTGTGTGGGGGGTGTGTGGGTGGGGGTGTGTGGGTGGGGGTGTGGGTGGGGGGTGTGTGGGTTGGGGTGTGAGGGTGGGGGGTGTGGGTGAGGTTGTGGGGTGAGGGTGTGGGTGAGGGTGTGTGGGGGAGGGTGTGGGTGGGGGTGGGGGGTGGGGGGGTGTGGCAGGGCCAGGCAAGTGAGGGTGTGAGGGTGGGGGTGTGAGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGGGGGTGTGTGGGTGAGGGTGTGGGTGAGGGTGTGGGTGAGG 60 PASS IMPRECISE;SVTYPE=INS;SVLEN=3518;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=175909995;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:562:0.06:0,0,1:47:3 - -2025-01-06 03:04:06,693 [DEBUG] Comparing chunk 143 -2025-01-06 03:04:06,693 [DEBUG] Made mat -> True 66.58869389776565 -> - chr6 46679539 SV_45 A . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-2559;END=46682104;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr6 46679539 severus_DEL6141 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=2560;END=46682099;STRANDS=+-;MAPQ=60;PHASESETID=46628780;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:398:0.48:0,0,1:55:50 - -2025-01-06 03:04:06,694 [DEBUG] Comparing chunk 144 -2025-01-06 03:04:06,694 [DEBUG] Made mat -> True 65.59344262295083 -> - chr6 70696489 SV_48 TTCTTCATTGACGCCTTGGCCTTTCAGGAGAATACTATTTAATTTCCATATATTTGTATAGTATCCATAGTTCTTCCTGTTATTGATTGCTAGTTTTATTCCATCATGGTCAGAGAAGATATTTG TCAA . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-121;END=70696613;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr6 70696488 severus_DEL6204 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=122;END=70696610;STRANDS=+-;MAPQ=60;PHASESETID=67616293;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:680:0.25:0,0,1:184:62 - -2025-01-06 03:04:06,695 [DEBUG] Comparing chunk 145 -2025-01-06 03:04:06,696 [DEBUG] Made mat -> True 65.93804745978659 -> - chr6 72397103 SV_49 AAGAGTAAATAGAAAGCTGAAAAAACCTGAGTAGAACTATAACTACCAGTATTTAACATTCTACTTACCAAAAAATGGGGAGAATACACCC A . SUBCLONAL SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-90;END=72397193;SUBCLONAL=y;COMPLEX=n;CIPOS1=0;CIPOS2=3;CIEND1=.;CIEND2=.;HOMLEN=3;HOMSEQ=AGA GT:PSL:PSO 0/1:.:. - chr6 72397103 severus_DEL6212 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=91;END=72397194;STRANDS=+-;MAPQ=60;PHASESETID=71221441;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:613:0.06:0,0,1:51:3 - -2025-01-06 03:04:06,697 [DEBUG] Comparing chunk 146 -2025-01-06 03:04:06,697 [DEBUG] Made mat -> True 66.65990088122614 -> - chr6 86269895 SV_50 G . SUBCLONAL-COMPLEX SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-9852;END=86279747;SUBCLONAL=y;COMPLEX=u;CIPOS1=0;CIPOS2=3;CIEND1=0;CIEND2=3;HOMLEN=3;HOMSEQ=TTT GT:PSL:PSO 0/1:.:. - chr6 86269895 severus_DEL6246 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=9853;END=86279748;STRANDS=+-;MAPQ=60;PHASESETID=84167793;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:664:0.07:0,0,1:56:4 - -2025-01-06 03:04:06,698 [DEBUG] Comparing chunk 147 -2025-01-06 03:04:06,698 [DEBUG] All FP -> False None -> - None chr6 131707581 severus_BND6342_1 N N]chr7:144186940] 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND6342_2;STRANDS=++;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/0:434:0.22:1,0,0:47:13 - -2025-01-06 03:04:06,699 [DEBUG] Comparing chunk 148 -2025-01-06 03:04:06,700 [DEBUG] chr6 157972793 SV_54 T T[chr11:125661474[ . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_177;CLUSTERID=cluster_4 GT:PSL:PSO 0/1:.:. - and chr6 157972793 severus_BND1296_2 N ]chr11:125661473]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1296_1;STRANDS=-+;MAPQ=60;PHASESETID=125584229|157821672;HP=2;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:541:0.69:0,0,1:28:62 - BND strand/direction mismatch -2025-01-06 03:04:06,700 [DEBUG] Made mat -> False None -> - chr6 157972793 SV_54 T T[chr11:125661474[ . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_177;CLUSTERID=cluster_4 GT:PSL:PSO 0/1:.:. - chr6 157972793 severus_BND1296_2 N ]chr11:125661473]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1296_1;STRANDS=-+;MAPQ=60;PHASESETID=125584229|157821672;HP=2;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:541:0.69:0,0,1:28:62 - -2025-01-06 03:04:06,701 [DEBUG] chr6 157972793 SV_54 T T[chr11:125661474[ . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_177;CLUSTERID=cluster_4 GT:PSL:PSO 0/1:.:. - and chr6 157972804 severus_BND1265_2 N [chr11:105902637[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1265_1;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;PHASESETID=105786144|157821672;HP=2;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:453:0.68:1,0,0:24:52 - BND join POS not within BNDDIST -2025-01-06 03:04:06,701 [DEBUG] Made mat -> False None -> - chr6 157972793 SV_54 T T[chr11:125661474[ . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=.;MATEID=SV_177;CLUSTERID=cluster_4 GT:PSL:PSO 0/1:.:. - chr6 157972804 severus_BND1265_2 N [chr11:105902637[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1265_1;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;PHASESETID=105786144|157821672;HP=2;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:453:0.68:1,0,0:24:52 - -2025-01-06 03:04:06,701 [DEBUG] chr6 157972805 SV_56 T [chr11:105902638[T . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=1;CIEND1=.;CIEND2=.;HOMLEN=1;HOMSEQ=G;MATEID=SV_178;CLUSTERID=cluster_4 GT:PSL:PSO 0|1:.,chr6*157972805*1:.,1 - and chr6 157972793 severus_BND1296_2 N ]chr11:125661473]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1296_1;STRANDS=-+;MAPQ=60;PHASESETID=125584229|157821672;HP=2;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:541:0.69:0,0,1:28:62 - BND join POS not within BNDDIST -2025-01-06 03:04:06,702 [DEBUG] Made mat -> False None -> - chr6 157972805 SV_56 T [chr11:105902638[T . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=1;CIEND1=.;CIEND2=.;HOMLEN=1;HOMSEQ=G;MATEID=SV_178;CLUSTERID=cluster_4 GT:PSL:PSO 0|1:.,chr6*157972805*1:.,1 - chr6 157972793 severus_BND1296_2 N ]chr11:125661473]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1296_1;STRANDS=-+;MAPQ=60;PHASESETID=125584229|157821672;HP=2;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:541:0.69:0,0,1:28:62 - -2025-01-06 03:04:06,702 [DEBUG] Made mat -> True 99.0 -> - chr6 157972805 SV_56 T [chr11:105902638[T . PASS SVTYPE=BND;EVENTTYPE=CHROMOPLEXY;SUBCLONAL=n;COMPLEX=y;CIPOS1=0;CIPOS2=1;CIEND1=.;CIEND2=.;HOMLEN=1;HOMSEQ=G;MATEID=SV_178;CLUSTERID=cluster_4 GT:PSL:PSO 0|1:.,chr6*157972805*1:.,1 - chr6 157972804 severus_BND1265_2 N [chr11:105902637[N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND1265_1;STRANDS=--;DETAILED_TYPE=inv_tra;MAPQ=60;PHASESETID=105786144|157821672;HP=2;CLUSTERID=severus_1 GT:GQ:VAF:hVAF:DR:DV 0/1:453:0.68:1,0,0:24:52 - -2025-01-06 03:04:06,703 [DEBUG] Comparing chunk 149 -2025-01-06 03:04:06,703 [DEBUG] All FP -> False None -> - None chr7 4824649 severus_BND6572_1 N N[chr7:7802513[ 60 PASS PRECISE;SVTYPE=BND;SVLEN=2977864;MATE_ID=severus_BND6572_2;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=4743880|6647929;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:629:0.3:0,1,0:128:54 - -2025-01-06 03:04:06,704 [DEBUG] Comparing chunk 150 -2025-01-06 03:04:06,704 [DEBUG] Made mat -> True 66.61195457976312 -> - chr7 6404812 SV_60 C . SUBCLONAL-COMPLEX SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-1217;END=6406029;SUBCLONAL=u;COMPLEX=u;CIPOS1=0;CIPOS2=3;CIEND1=0;CIEND2=3;HOMLEN=3;HOMSEQ=GTG GT:PSL:PSO 0/1:.:. - chr7 6404812 severus_DEL6577 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=1218;END=6406030;STRANDS=+-;MAPQ=60;PHASESETID=6215117;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:843:0.18:0,1,0:120:26 - -2025-01-06 03:04:06,705 [DEBUG] Comparing chunk 151 -2025-01-06 03:04:06,705 [DEBUG] Made mat -> True 63.63495024875622 -> - chr7 6408188 SV_61 CACACCACCACACCTGGCTAATTTTTGTATTTTTAGTAGAGACGGGTTTCACCATGTTGGCCAGGCT CTATA . COMPLEX SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-62;END=6408254;SUBCLONAL=n;COMPLEX=u;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr7 6408192 severus_DEL6578 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=64;END=6408256;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=6215117;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:741:0.21:0,1,0:136:37 - -2025-01-06 03:04:06,706 [DEBUG] Comparing chunk 152 -2025-01-06 03:04:06,706 [DEBUG] All FP -> False None -> - None chr7 7802513 severus_BND6572_2 N ]chr7:4824649]N 60 PASS PRECISE;SVTYPE=BND;SVLEN=2977864;MATE_ID=severus_BND6572_1;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=4743880|6647929;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:629:0.3:0,1,0:128:54 - -2025-01-06 03:04:06,706 [DEBUG] Comparing chunk 153 -2025-01-06 03:04:06,707 [DEBUG] Made mat -> True 66.50812502356446 -> - chr7 19196736 SV_62 AAGATCCAAAATTGACACCCTAACATCACAATTAAAAGAACTAGAAAAGCAAGAGCAGACACATTCAAAAGCTAGCAGAAGGCAAGAAATAACGAAAATCAGAGCAGAACTGAAGGAAATAGAGACACAAAAAACCCTTCAAAAAATTAATGAATCCAGGAGCTGGTTTTTTGAAAGGATCAACAAAATTGATAGACCACTAGCAAGACTAATAAAGAAAAAAAGACAGAAGAATCAAATAGACGCAAAAAAAATGATAAAGGGGATATCATCACTGATCCCACAGAAATACGAACTACCATCAGAGAATACTACAAACACCTCTATGCAAATAAACTAGAAAATCTAGAAGAAATGGATAAATTCCTCGACACATACACTCTCCCAAGACTAAACCAGGAAGAAGTTGAATCTCTGAAT A . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-419;END=19197155;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=3;CIEND1=.;CIEND2=.;HOMLEN=3;HOMSEQ=AGA GT:PSL:PSO 0/1:.:. - chr7 19196736 severus_DEL6614 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=420;END=19197156;STRANDS=+-;MAPQ=60;PHASESETID=19068527;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:590:0.32:0,1,0:100:48 - -2025-01-06 03:04:06,708 [DEBUG] Comparing chunk 154 -2025-01-06 03:04:06,708 [DEBUG] All FP -> False None -> - None chr7 23502990 severus_INS17816 N 60 PASS PRECISE;SVTYPE=INS;SVLEN=132;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=23016499;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:1061:0.05:0,0,1:88:5 - -2025-01-06 03:04:06,709 [DEBUG] Comparing chunk 155 -2025-01-06 03:04:06,709 [DEBUG] Made mat -> True 33.337554345532055 -> - chr7 68922689 SV_64 A . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=7896;END=68930585;SUBCLONAL=y;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr7 68922689 severus_INV6732 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=7896;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=68769190;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:498:0.13:0,1,0:46:7 - -2025-01-06 03:04:06,709 [DEBUG] chr7 68927903 SV_65 T . SUBCLONAL SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=19026;END=68946929;SUBCLONAL=y;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr7 68922689 severus_INV6732 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=7896;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=68769190;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:498:0.13:0,1,0:46:7 - are not the same SVTYPE -2025-01-06 03:04:06,710 [DEBUG] chr7 68927903 SV_65 T . SUBCLONAL SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=19026;END=68946929;SUBCLONAL=y;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr7 68922689 severus_INV6732 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=7896;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=68769190;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:498:0.13:0,1,0:46:7 - are not within REFDIST -2025-01-06 03:04:06,710 [DEBUG] chr7 68927903 SV_65 T . SUBCLONAL SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=19026;END=68946929;SUBCLONAL=y;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - and chr7 68922689 severus_INV6732 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=7896;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=68769190;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:498:0.13:0,1,0:46:7 - size similarity is too low (0.415) -2025-01-06 03:04:06,710 [DEBUG] Made mat -> False 13.833701250919795 -> - chr7 68927903 SV_65 T . SUBCLONAL SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=19026;END=68946929;SUBCLONAL=y;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr7 68922689 severus_INV6732 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=7896;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=68769190;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:498:0.13:0,1,0:46:7 - -2025-01-06 03:04:06,711 [DEBUG] chr7 68930591 SV_67 G . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=19722;END=68950313;SUBCLONAL=y;COMPLEX=y;CIPOS1=0;CIPOS2=2;CIEND1=-2;CIEND2=0;HOMLEN=2;HOMSEQ=CA GT:PSL:PSO 0/1:.:. - and chr7 68922689 severus_INV6732 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=7896;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=68769190;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:498:0.13:0,1,0:46:7 - are not within REFDIST -2025-01-06 03:04:06,711 [DEBUG] chr7 68930591 SV_67 G . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=19722;END=68950313;SUBCLONAL=y;COMPLEX=y;CIPOS1=0;CIPOS2=2;CIEND1=-2;CIEND2=0;HOMLEN=2;HOMSEQ=CA GT:PSL:PSO 0/1:.:. - and chr7 68922689 severus_INV6732 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=7896;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=68769190;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:498:0.13:0,1,0:46:7 - size similarity is too low (0.400) -2025-01-06 03:04:06,711 [DEBUG] Made mat -> False 13.345502484535038 -> - chr7 68930591 SV_67 G . SUBCLONAL-COMPLEX SVTYPE=INV;EVENTTYPE=INV;SVLEN=19722;END=68950313;SUBCLONAL=y;COMPLEX=y;CIPOS1=0;CIPOS2=2;CIEND1=-2;CIEND2=0;HOMLEN=2;HOMSEQ=CA GT:PSL:PSO 0/1:.:. - chr7 68922689 severus_INV6732 N 60 PASS PRECISE;SVTYPE=INV;SVLEN=7896;STRANDS=++;DETAILED_TYPE=foldback;MAPQ=60;PHASESETID=68769190;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:498:0.13:0,1,0:46:7 - -2025-01-06 03:04:06,712 [DEBUG] Comparing chunk 156 -2025-01-06 03:04:06,713 [DEBUG] All FP -> False None -> - None chr7 75988864 severus_DEL6755 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=50;END=75988914;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=75361827;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:268:0.14:0,1,0:25:4 - -2025-01-06 03:04:06,714 [DEBUG] Comparing chunk 157 -2025-01-06 03:04:06,714 [DEBUG] All FP -> False None -> - None chr7 144186940 severus_BND6342_2 N N]chr6:131707581] 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND6342_1;STRANDS=++;MAPQ=60;PHASESETID=131523827|143703888;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:434:0.22:1,0,0:47:13 - -2025-01-06 03:04:06,715 [DEBUG] Comparing chunk 158 -2025-01-06 03:04:06,715 [DEBUG] Made mat -> True 66.26384325179507 -> - chr7 154017977 SV_68 TCTGGCAGAGTGCAGGGCCAGATGAAATTCACATGAAGGAGGAACACCTGATCTGTATGGCCCTGTCATTATTATGCATACCCATGGAACCAGCTGGGCACTCAGGGTTATATGTGGTAGCCACAGCAGGGTGATTTGCAACCCCCACTCCTATATCCATCAAGA T . SUBCLONAL SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-164;END=154018141;SUBCLONAL=y;COMPLEX=n;CIPOS1=0;CIPOS2=1;CIEND1=.;CIEND2=.;HOMLEN=1;HOMSEQ=C GT:PSL:PSO 0/1:.:. - chr7 154017977 severus_DEL6931 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=165;END=154018142;STRANDS=+-;MAPQ=60;PHASESETID=153798083;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:613:0.11:0,0,1:55:7 - -2025-01-06 03:04:06,716 [DEBUG] Comparing chunk 159 -2025-01-06 03:04:06,716 [DEBUG] All FP -> False None -> - None chr7 158151451 severus_INS18300 N CCTTTCTGCTCCTGCCTCTCCCTGCCCACACCGCCCGCCTTTCTATTCCTGCCTCTCCCTGCCCACACCGCCCGCCTTTCTATTCCTGCCTCTCCCTGCCCACACCGCCCGCCTTTCTATTCCTGCCTCTCCCTGCCCATATCGCCCGCCTTTCTGCTCCTGCCTCTCCCTGCCCACACCGCCCGCCTTCTATTCTTGCCTCTCCCTGCCCACACCGCCCGCCTTTCTGCTCCTGCCTCTCCCTGCCCACACTGCTCACCTTTCTATTCCTGCCTCTCCCTGCCCACATCACCCGCCTTTCTGCTCCTGCCCCTGCCTGCCCACACCGCCCA 60 PASS IMPRECISE;SVTYPE=INS;SVLEN=350;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=157781762;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:447:0.09:0,1,0:39:4 - -2025-01-06 03:04:06,716 [DEBUG] Comparing chunk 160 -2025-01-06 03:04:06,717 [DEBUG] Made mat -> True 65.82805907172997 -> - chr8 3671496 SV_69 CATATATATATATATATGATCATATATATGATCATATATATATATATATGATCATATATATGATCATATATATATATAT C . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-78;END=3671574;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=16;CIEND1=.;CIEND2=.;HOMLEN=16;HOMSEQ=ATATATATATATATAT GT:PSL:PSO 0/1:.:. - chr8 3671496 severus_DEL7039 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=79;END=3671575;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=3134598;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:310:0.5:0,1,0:43:43 - -2025-01-06 03:04:06,718 [DEBUG] Comparing chunk 161 -2025-01-06 03:04:06,718 [DEBUG] All FP -> False None -> - None chr8 48193109 severus_DEL7132 N 60 PASS IMPRECISE;SVTYPE=DEL;SVLEN=86;END=48193195;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/0:895:0.05:0,1,1:74:4 - -2025-01-06 03:04:06,718 [DEBUG] Comparing chunk 162 -2025-01-06 03:04:06,719 [DEBUG] Made mat -> True 66.07928375511048 -> - chr8 67457351 SV_70 AATTCTCATTTTTTTCCTGTCTATTAAGATTCTTTGGTTTTTGGTCAAAGCCCTTTAACTGGATATATGGGGGACTTATTTTTTTGGCTGAAGATCTTGGAGTCTTCAGCTCC A . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-112;END=67457463;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=1;CIEND1=.;CIEND2=.;HOMLEN=1;HOMSEQ=A GT:PSL:PSO 0/1:.:. - chr8 67457351 severus_DEL7166 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=113;END=67457464;STRANDS=+-;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/1:616:0.3:0,1,1:104:45 - -2025-01-06 03:04:06,719 [DEBUG] Comparing chunk 163 -2025-01-06 03:04:06,720 [DEBUG] Made mat -> True 66.65209312475758 -> - chr8 75063364 SV_71 T . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-4573;END=75067937;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chr8 75063364 severus_DEL7183 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=4574;END=75067938;STRANDS=+-;MAPQ=60;PHASESETID=73263743;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:603:0.32:0,1,0:124:58 - -2025-01-06 03:04:06,722 [DEBUG] Comparing chunk 164 -2025-01-06 03:04:06,722 [DEBUG] All FN -> False None -> - chr8 77023607 SV_72 T . SUBCLONAL SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-16819;END=77040432;SUBCLONAL=y;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - None -2025-01-06 03:04:06,723 [DEBUG] Comparing chunk 165 -2025-01-06 03:04:06,723 [DEBUG] Made mat -> True 66.66666666666666 -> - chr8 104941340 SV_73 T TCATAGTTACTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAAAATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATATCCTTTGTAGGGACATGGATGAAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAAC . PASS SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=387;END=104941340;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=14;CIEND1=.;CIEND2=.;HOMLEN=14;HOMSEQ=CATAGTTACTTTTA GT:PSL:PSO 0/1:.:. - chr8 104941340 severus_INS18694 N CATAGTTACTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAAAATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATATCCTTTGTAGGGACATGGATGAAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAAC 60 PASS PRECISE;SVTYPE=INS;SVLEN=387;MAPQ=60;PHASESETID=104938122;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:603:0.31:0,0,1:123:56 - -2025-01-06 03:04:06,724 [DEBUG] Comparing chunk 166 -2025-01-06 03:04:06,725 [DEBUG] Made mat -> True 66.48957091152535 -> - chr8 107947965 SV_74 A AAATGATCTCCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCACTGCACCCACTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACTATAAACTACCATCAG . PASS SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=564;END=107947965;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=16;CIEND1=0;CIEND2=16;HOMLEN=16;HOMSEQ=AATGATCTCCCTTTTT GT:PSL:PSO 0/1:.:. - chr8 107947965 severus_INS18702 N AATGATCTCCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCACTGCACCCACTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCCTCCCCCGACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTACAAAGGGCTAATATCCAGAATCTACAATGAACTCAAACAAATTTACAAGAAAAAAACAAACAACCCCATCAAAAAGTGGGCGAAGGACATGAACAGACACTTCTCAAAAGAAGACATTTATGCAGCCAAAAAACACATGAAGAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACTATAAACTACCATCAG 60 PASS PRECISE;SVTYPE=INS;SVLEN=563;MAPQ=60;PHASESETID=107410651;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:616:0.3:0,0,1:105:46 - -2025-01-06 03:04:06,725 [DEBUG] Comparing chunk 167 -2025-01-06 03:04:06,726 [DEBUG] All FP -> False None -> - None chr8 143669360 severus_INS18861 N 60 PASS PRECISE;SVTYPE=INS;SVLEN=168;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=143662218;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:856:0.11:0,0,1:76:9 - -2025-01-06 03:04:06,727 [DEBUG] Comparing chunk 168 -2025-01-06 03:04:06,727 [DEBUG] Made mat -> True 66.66330856734875 -> - chr9 21952492 SV_75 T . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-19851;END=21972343;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=5;CIEND1=0;CIEND2=5;HOMLEN=5;HOMSEQ=AGGGA GT:PSL:PSO 0/1:.:. - chr9 21952492 severus_DEL7407 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=19852;END=21972344;STRANDS=+-;MAPQ=60;PHASESETID=21602753;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:411:0.54:0,1,0:52:62 - -2025-01-06 03:04:06,728 [DEBUG] Comparing chunk 169 -2025-01-06 03:04:06,728 [DEBUG] All FP -> False None -> - None chr9 104414095 severus_INS19176 N TAACAGGTGCTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTCTTTTTCTTTCTTTTTTTTTTTTTTTATTATACTCTAAGTTTTAGGGTACATGTGCACATTGTGCAGGTTAGTTACATATGTATACATGTGCCATGCTGGTGCGCTGCACCCACTAATGTGTCATCTAGCATTAGGTATATCTCCCAATGCTATCCCTCCCCCTCCCCCTACCCCACCACAGTCCCCAGAGTGTGATATTCCCCTTCCTGTGTCCATGTGATCTCATTGTTCAATTCCCACCTATGAGTGAGAATATGCGGTGTTTGGTTTTTTGTTCTTGCGATAGTTTACTGAGAATGATGGTTTCCAATTTCATCCATGTCCCTACAAAGGATATGAACTCATCATTTTTTATGGCTGCATAGTATTCCATGGTGTATATGTGCCACATTTTCTTAATCCAGTCTATCATTGTTGGACATTTGGGTTGGTTCCAAGTCTTTGCTATTGTGAATAGTGCCGCAATAAACATACGTGTGCATGTGTCTTTATAGCAGCATGATTTATACTCATTTGGGTATATACCCAGTAATGGGATGGCTGGGTCAAATGGTATTTCTAGTTCTAGATCCCTGAGGAATCGCCACACTGACTTCCACAATGCACATGAAGAAATGCTCATCATCACTGGCCATCAGAGAAATGCAAATCAAAACCACTATGAGATATCATCTCACACCAGTTAGAATGGCAATCATTAAAAAGTCAGGAAACAACAGGTGCTGGAGAGGATGCGGAGAAATAGGAACACTTT 60 PASS PRECISE;SVTYPE=INS;SVLEN=817;MAPQ=60;PHASESETID=104059409;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:831:0.08:0,1,0:71:6 - -2025-01-06 03:04:06,729 [DEBUG] Comparing chunk 170 -2025-01-06 03:04:06,730 [DEBUG] All FP -> False None -> - None chr9 136535727 severus_INS19358 N CACTCAGGATCCCTCCCGGGGCAATGGGTGCAGGGTGGGAGTGGGTGGAGGGGGAGCACTCAGGATCCCTCCCGGGGCAATGGGTGCAGGGTGGGAGTGGGTGGGAGGGGGAGCACTCAGGATCCCTCCTGGGGCAATGGGTGCAGGGTGGGAGTGGGTGGAGGGGGGATCACTCAGGATCCCTCCCGGGGCAATGGGTGCAGGGTGGGAGTGGGTGGAGGGGGGATCACTCAGGATCCCTCCCGGGGCAATGGGTGCAGGGTGGGAGTGGGTGGAGGGGGGAGCACTCAGGATCCCTCCCGGGGCAATGGGTGCAGGGTGGGAGTGGGTGGAGGGGGAGCACTCAGGATCCCTCCTGGGGCAATGGGTGCAGGGTGGGTGGAGAGGGGAGGTGGGTCGGGGGGAGCACTCAGGATCCCTCCCGGGGCAATGGGTGCAGGGTGGGTGGAGAGGGGAGCACTCAGGATCCCTCCCAGGGGCAATGGGTGCAGGGTGGGTCGGGGGGAGCACTCAGGATCCCTCCCGGGGCAATGGGTGCAGGGTGGGTGGAGAGGGGAGCACTCAGGATCCCTCCCGGGGCAATGGGTGCAGGGTGGGTGGAGAGGGGAGCACTCAGGATCCCTCCTGGGGCAATGGGTGCATGGTGGGTGGGGGGGAGCACTCAGGATCCCTCCCAGGGGCAATGGGTGCAGGGTGGGTGGAGGGGGATCACTCAGGATCCCTCCCAGGGGCAATGGGTGCAGGGTGGGAGTGGGTGGAGGGGGGAGCACTCAGGATCCCTCCCAGGGGCAATGGGTGCAGGGTGGGTGGAGGGGGGATCACTCAGGATCCCTCCCAGGGGCAATGGGTGCAGGGTGGGAGTGGGTGGAGGGGGAGCACTCAGGATCCCTCCCGGGGCAATGAGTGCAGGGTGGGTGGAGAGGGGAGCACTCAGGATCCCTCCTGGGGCAATGGGTGCAGGGTGGGTGGAGAGGGGAGCACTCAGGATCCTCCTGGGGCAATGGGTGCATGGTGGGTGGGGGGGAGCACTCAGGATCCCTCCCGGGCAATGGGTGCAGGGTGGGTGGAGAGGGGAGCACTCAGGATCCCTCCCAGGGGCAATGGGTGCAGGGTGGGTCGGGGGGAGCACTCAGGATCCCTCCCGGGGCAATGGGTGCAGGGTGGGTGGAGAGGGGAGCACTCAGGATCCCTCCCGGGGCAATGGGTGCAGGGTGGGTGGAGAGGGGAGCACTCAGGATCCCTCCTGGGGCAATGGGTGCATGGTGGGTGGGGGGGAGCACTCAGGATCCCTCCCAGGGGCAATGGGTGCAGGGTGGGTGGAGGGGGGATCACTCAGGATCCCTCCCAGGGGCAATGGGTGCAGGGTGGGA 60 PASS PRECISE;SVTYPE=INS;SVLEN=1372;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=136162084;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:370:0.11:0,0,1:33:4 - -2025-01-06 03:04:06,730 [DEBUG] Comparing chunk 171 -2025-01-06 03:04:06,731 [DEBUG] Made mat -> True 100.0 -> - chrX 8495892 SV_160 N N[chr2:89324414[ . SUBCLONAL-COMPLEX SVTYPE=BND;EVENTTYPE=BND;SUBCLONAL=u;COMPLEX=y;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chrX 8495892 severus_BND7781_1 N N[chr2:89324414[ 55.5 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND7781_2;STRANDS=-+;MAPQ=55;PHASESETID=8341569|89204393;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:641:0.29:0,0,1:74:30 - -2025-01-06 03:04:06,731 [DEBUG] Comparing chunk 172 -2025-01-06 03:04:06,732 [DEBUG] Made mat -> True 66.66666666666666 -> - chrX 8514918 SV_161 A . SUBCLONAL-COMPLEX SVTYPE=DUP;EVENTTYPE=DUP;SVLEN=2837;END=8517755;SUBCLONAL=u;COMPLEX=y;CIPOS1=0;CIPOS2=1;CIEND1=0;CIEND2=1;HOMLEN=1;HOMSEQ=A GT:PSL:PSO 0/1:.:. - chrX 8514918 severus_DUP7782 N 60 PASS PRECISE;SVTYPE=DUP;SVLEN=2837;END=8517755;STRANDS=-+;DETAILED_TYPE=tandem_duplication;MAPQ=60;PHASESETID=8341569;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:818:0.18:0,0,1:106:24 - -2025-01-06 03:04:06,733 [DEBUG] Comparing chunk 173 -2025-01-06 03:04:06,733 [DEBUG] Made mat -> True 66.62072377721233 -> - chrX 24130816 SV_162 A . PASS SVTYPE=DUP;EVENTTYPE=DUP:TANDEM;SVLEN=28295;END=24159111;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=17;CIEND1=0;CIEND2=17;HOMLEN=17;HOMSEQ=TCCCAAGTAGCTGGGAC GT:PSL:PSO 0/1:.:. - chrX 24130855 severus_DUP7803 N 60 PASS PRECISE;SVTYPE=DUP;SVLEN=28295;END=24159150;STRANDS=-+;DETAILED_TYPE=tandem_duplication;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/1:680:0.26:1,0,0:104:36 - -2025-01-06 03:04:06,734 [DEBUG] Comparing chunk 174 -2025-01-06 03:04:06,734 [DEBUG] Made mat -> True 66.55586141970927 -> - chrX 34245830 SV_163 A . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-2406;END=34248236;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chrX 34245828 severus_DEL7819 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=2403;END=34248231;STRANDS=+-;MAPQ=60;PHASESETID=33254341;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:590:0.32:0,1,0:71:34 - -2025-01-06 03:04:06,735 [DEBUG] Comparing chunk 175 -2025-01-06 03:04:06,735 [DEBUG] Made mat -> True 66.66666666666666 -> - chrX 44845879 SV_164 CCAGCTACTCGGGAGGCTGAGGCAAGAGAAGCACTTGAACCCGGAAGGTGGAGGTTGCAGTGAGCCAAGAGCACGCCATTGCACTCCAGCCTTGGGTGACAGAGCGAGACTCCGTCTC CT . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-117;END=44845996;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chrX 44845879 severus_DEL7829 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=117;END=44845996;STRANDS=+-;MAPQ=60;PHASESETID=44838943;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/1:590:0.33:0,0,1:86:42 - -2025-01-06 03:04:06,736 [DEBUG] Comparing chunk 176 -2025-01-06 03:04:06,737 [DEBUG] Made mat -> True 66.66666666666666 -> - chrX 69807092 SV_165 T TAAAAAAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATATCCTTTGTAGGGACATGGATGAAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAACACCGCATATTCTCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTCGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACACATTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA . PASS SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=513;END=69807092;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=5;CIEND1=0;CIEND2=5;HOMLEN=5;HOMSEQ=AAAAA GT:PSL:PSO 0/1:.:. - chrX 69807092 severus_INS19678 N AAAAAAAAGACTTGGAACCAACCCAAATGTCCAACAATGATAGACTGGATTAAGAAAATGTGGCACATATACACCATGGAATACTATGCAGCCATAAAAAATGATGAGTTCATATCCTTTGTAGGGACATGGATGAAATTGGAAACCATCATTCTCAGTAAACTATCGCAAGAACAAAAAACCAAACACCGCATATCTCACTCATAGGTGGGAATTGAACAATGAGATCACATGGACACAGGAAGGGGAATATCACACTCTGGGGACTGTGGTGGGGTCGGGGGGAGGGGGGAGGGATAGCATTGGGAGATATACCTAATGCTAGATGACACATTAGTGGGTGCAGCGCACCAGCATGGCACATGTATACATATGTAACTAACCTGCACAATGTGCACATGTACCCTAAAACTTAGAGTATAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 60 PASS PRECISE;SVTYPE=INS;SVLEN=513;MAPQ=60;PHASESETID=69204502;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:629:0.3:0,1,0:124:52 - -2025-01-06 03:04:06,738 [DEBUG] Comparing chunk 177 -2025-01-06 03:04:06,738 [DEBUG] Made mat -> True 66.62413609349292 -> - chrX 79649369 SV_166 C . PASS SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=-1566;END=79650935;SUBCLONAL=n;COMPLEX=n;CIPOS1=0;CIPOS2=2;CIEND1=0;CIEND2=2;HOMLEN=2;HOMSEQ=CT GT:PSL:PSO 0/1:.:. - chrX 79649369 severus_DEL7869 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=1567;END=79650936;STRANDS=+-;MAPQ=60;PHASESETID=78725775;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:641:0.29:0,1,0:104:42 - -2025-01-06 03:04:06,739 [DEBUG] Comparing chunk 178 -2025-01-06 03:04:06,739 [DEBUG] All FP -> False None -> - None chrX 90627649 severus_BND7887_1 N N[chrX:95207240[ 60 PASS PRECISE;SVTYPE=BND;SVLEN=4579591;MATE_ID=severus_BND7887_2;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=90013859|94985097;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:818:0.19:0,1,0:116:27 - -2025-01-06 03:04:06,740 [DEBUG] Comparing chunk 179 -2025-01-06 03:04:06,740 [DEBUG] All FP -> False None -> - None chrX 95207240 severus_BND7887_2 N ]chrX:90627649]N 60 PASS PRECISE;SVTYPE=BND;SVLEN=4579591;MATE_ID=severus_BND7887_1;STRANDS=-+;DETAILED_TYPE=Templated_ins;MAPQ=60;PHASESETID=90013859|94985097;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/0:818:0.19:0,1,0:116:27 - -2025-01-06 03:04:06,740 [DEBUG] Comparing chunk 180 -2025-01-06 03:04:06,741 [DEBUG] All FP -> False None -> - None chrX 95810802 severus_BND2999_2 N ]chr18:28482570]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2999_1;STRANDS=-+;DETAILED_TYPE=Reciprocal_tra;MAPQ=60;PHASESETID=27941033|95455414;HP=1;CLUSTERID=severus_7 GT:GQ:VAF:hVAF:DR:DV 0/1:324:0.53:1,0,0:38:43 - -2025-01-06 03:04:06,741 [DEBUG] Comparing chunk 181 -2025-01-06 03:04:06,741 [DEBUG] All FP -> False None -> - None chrX 95812868 severus_BND2998_2 N N[chr18:28481423[ 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND2998_1;STRANDS=+-;DETAILED_TYPE=Reciprocal_tra;MAPQ=60;PHASESETID=27941033|95455414;HP=1;CLUSTERID=severus_7 GT:GQ:VAF:hVAF:DR:DV 0/1:361:0.55:1,0,0:39:47 - -2025-01-06 03:04:06,742 [DEBUG] Comparing chunk 182 -2025-01-06 03:04:06,742 [DEBUG] Made mat -> True 60.573915408676726 -> - chrX 125899652 SV_169 ATAAG ATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTCTTCTTTGTTTTATTTTTCTTTTTTTTTTTTTTTTTTTTTTTTT . PASS SVTYPE=INS;EVENTTYPE=INS:ME;SVLEN=129;END=125899656;SUBCLONAL=n;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chrX 125899652 severus_INS19816 N TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTCTTCTTTGTTTTATTTTTCTTTTTTTTTTTTTTTTTTTTTT 60 PASS IMPRECISE;SVTYPE=INS;SVLEN=119;MAPQ=60;PHASESETID=125319126;HP=1 GT:GQ:VAF:hVAF:DR:DV 0/1:539:0.37:0,1,0:90:52 - -2025-01-06 03:04:06,743 [DEBUG] Comparing chunk 183 -2025-01-06 03:04:06,743 [DEBUG] All FP -> False None -> - None chrX 125901255 severus_DEL7938 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=122;END=125901377;STRANDS=+-;MAPQ=60;PHASESETID=125319126;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:984:0.06:0,0,1:82:5 - -2025-01-06 03:04:06,744 [DEBUG] Comparing chunk 184 -2025-01-06 03:04:06,744 [DEBUG] Made mat -> True 66.66666666666666 -> - chrX 144037790 SV_170 N . SUBCLONAL SVTYPE=DEL;EVENTTYPE=DEL;SVLEN=121;END=144037911;SUBCLONAL=y;COMPLEX=n;CIPOS1=.;CIPOS2=.;CIEND1=.;CIEND2=.;HOMLEN=.;HOMSEQ=. GT:PSL:PSO 0/1:.:. - chrX 144037790 severus_DEL7968 N 60 PASS PRECISE;SVTYPE=DEL;SVLEN=121;END=144037911;STRANDS=+-;INSIDE_VNTR=TRUE;MAPQ=60;PHASESETID=144014072;HP=2 GT:GQ:VAF:hVAF:DR:DV 0/0:920:0.05:0,0,1:76:4 - -2025-01-06 03:04:06,745 [INFO] Zipped 418 variants Counter({'comp': 243, 'base': 175}) -2025-01-06 03:04:06,745 [INFO] 185 chunks of 418 variants Counter({'comp': 190, '__filtered': 115, 'base': 113}) -2025-01-06 03:04:06,745 [DEBUG] Comparing chunk 185 -2025-01-06 03:04:06,746 [DEBUG] All FP -> False None -> - None chrY 9591886 severus_BND8004_1 N ]chr11:33648576]N 60 PASS PRECISE;SVTYPE=BND;MATE_ID=severus_BND8004_2;STRANDS=+-;MAPQ=60 GT:GQ:VAF:hVAF:DR:DV 0/0:524:0.1:1,0,0:46:5 - -2025-01-06 03:04:06,823 [INFO] Stats: { +2025-01-08 19:03:15,294 [WARNING] 193 contigs present in comparison VCF header are not in baseline VCF. +2025-01-08 19:03:15,364 [INFO] Zipped 418 variants Counter({'comp': 243, 'base': 175}) +2025-01-08 19:03:15,365 [INFO] 185 chunks of 418 variants Counter({'comp': 190, '__filtered': 115, 'base': 113}) +2025-01-08 19:03:15,412 [INFO] Stats: { "TP-base": 85, "TP-comp": 85, "FP": 81, @@ -1163,4 +64,4 @@ } } } -2025-01-06 03:04:06,823 [INFO] Finished bench +2025-01-08 19:03:15,412 [INFO] Finished bench diff --git a/repo_utils/answer_key/bench/bench_bnd/params.json b/repo_utils/answer_key/bench/bench_bnd/params.json index b2fd5f1c..a1df56f0 100644 --- a/repo_utils/answer_key/bench/bench_bnd/params.json +++ b/repo_utils/answer_key/bench/bench_bnd/params.json @@ -1 +1 @@ -{"base": "/data/repo_utils/test_files/variants/bnd.base.vcf.gz", "comp": "/data/repo_utils/test_files/variants/bnd.comp.vcf.gz", "output": "test_results/bench_bnd/", "includebed": null, "extend": 0, "debug": true, "reference": null, "refdist": 500, "pctseq": 0.0, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "HG008-T", "cSample": "HG008_T_hiphase.haplotagged", "dup_to_ins": false, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "check_monref": true, "check_multi": true} \ No newline at end of file +{"base": "/Users/english/code/truvari/repo_utils/test_files/variants/bnd.base.vcf.gz", "comp": "/Users/english/code/truvari/repo_utils/test_files/variants/bnd.comp.vcf.gz", "output": "test_results/bench_bnd/", "includebed": null, "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.0, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "HG008-T", "cSample": "HG008_T_hiphase.haplotagged", "dup_to_ins": false, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 50000, "passonly": false, "no_ref": false, "pick": "single", "ignore_monref": true, "check_multi": true, "check_monref": true, "no_single_bnd": true, "write_resolved": false, "decompose": false, "short_circuit": false, "skip_gt": false} \ No newline at end of file diff --git a/repo_utils/answer_key/bench/bench_bnd/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench_bnd/tp-base.vcf.gz index 3e0a70c0..de3e4082 100644 Binary files a/repo_utils/answer_key/bench/bench_bnd/tp-base.vcf.gz and b/repo_utils/answer_key/bench/bench_bnd/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_bnd/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_bnd/tp-base.vcf.gz.tbi index d015e02a..f4aee1a3 100644 Binary files a/repo_utils/answer_key/bench/bench_bnd/tp-base.vcf.gz.tbi and b/repo_utils/answer_key/bench/bench_bnd/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_bnd/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench_bnd/tp-comp.vcf.gz index 7acfd454..443da481 100644 Binary files a/repo_utils/answer_key/bench/bench_bnd/tp-comp.vcf.gz and b/repo_utils/answer_key/bench/bench_bnd/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_bnd/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_bnd/tp-comp.vcf.gz.tbi index 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a/repo_utils/answer_key/bench/bench_bnd_decomp/fn.vcf.gz b/repo_utils/answer_key/bench/bench_bnd_decomp/fn.vcf.gz new file mode 100644 index 00000000..ef5bed6e Binary files /dev/null and b/repo_utils/answer_key/bench/bench_bnd_decomp/fn.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_bnd_decomp/fn.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_bnd_decomp/fn.vcf.gz.tbi new file mode 100644 index 00000000..41d2b0c6 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_bnd_decomp/fn.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_bnd_decomp/fp.vcf.gz b/repo_utils/answer_key/bench/bench_bnd_decomp/fp.vcf.gz new file mode 100644 index 00000000..bcf98066 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_bnd_decomp/fp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_bnd_decomp/fp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_bnd_decomp/fp.vcf.gz.tbi new file mode 100644 index 00000000..98333e58 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_bnd_decomp/fp.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_bnd_decomp/log.txt b/repo_utils/answer_key/bench/bench_bnd_decomp/log.txt new file mode 100644 index 00000000..6203efea --- /dev/null +++ b/repo_utils/answer_key/bench/bench_bnd_decomp/log.txt @@ -0,0 +1,66 @@ +2025-01-08 18:56:46,711 [INFO] Truvari v5.0.0 +2025-01-08 18:56:46,711 [INFO] Command /Users/english/code/truvari/truvari/__main__.py bench -b repo_utils/test_files/variants/bnd.base.vcf.gz -c repo_utils/test_files/variants/bnd.comp2.vcf.gz --sizemax 1000000000 -p 0 --pick multi -o test_results/bench_bnd_decomp/ +2025-01-08 18:56:46,711 [INFO] Params: +{ + "base": "/Users/english/code/truvari/repo_utils/test_files/variants/bnd.base.vcf.gz", + "comp": "/Users/english/code/truvari/repo_utils/test_files/variants/bnd.comp2.vcf.gz", + "output": "test_results/bench_bnd_decomp/", + "includebed": null, + "extend": 0, + "debug": false, + "reference": null, + "refdist": 500, + "pctseq": 0.0, + "pctsize": 0.7, + "pctovl": 0.0, + "typeignore": false, + "no_roll": true, + "chunksize": 1000, + "bSample": "HG008-T", + "cSample": "HG008_NP_PB_germline", + "dup_to_ins": false, + "bnddist": 100, + "sizemin": 50, + "sizefilt": 30, + "sizemax": 1000000000, + "passonly": false, + "no_ref": false, + "pick": "multi", + "ignore_monref": true, + "check_multi": true, + "check_monref": true, + "no_single_bnd": true, + "write_resolved": false, + "decompose": true, + "short_circuit": false, + "skip_gt": false +} +2025-01-08 18:56:46,741 [WARNING] 193 contigs present in comparison VCF header are not in baseline VCF. +2025-01-08 18:56:52,141 [INFO] Zipped 30077 variants Counter({'comp': 29902, 'base': 175}) +2025-01-08 18:56:52,141 [INFO] 20652 chunks of 30077 variants Counter({'comp': 29902, 'base': 170, '__filtered': 5}) +2025-01-08 18:56:55,373 [INFO] Stats: { + "TP-base": 137, + "TP-comp": 129, + "FP": 28401, + "FN": 33, + "precision": 0.00452155625657203, + "recall": 0.8058823529411765, + "f1": 0.0089926574974431, + "base cnt": 170, + "comp cnt": 28530, + "TP-comp_TP-gt": 1, + "TP-comp_FP-gt": 128, + "TP-base_TP-gt": 1, + "TP-base_FP-gt": 136, + "gt_concordance": 0.007751937984496124, + "gt_matrix": { + "(0, 1)": { + "(0, 0)": 134, + "(0, 1)": 1 + }, + "(1, 0)": { + "(0, 0)": 2 + } + } +} +2025-01-08 18:56:55,373 [INFO] Finished bench diff --git a/repo_utils/answer_key/bench/bench_bnd_decomp/params.json b/repo_utils/answer_key/bench/bench_bnd_decomp/params.json new file mode 100644 index 00000000..d2032953 --- /dev/null +++ b/repo_utils/answer_key/bench/bench_bnd_decomp/params.json @@ -0,0 +1 @@ +{"base": "/Users/english/code/truvari/repo_utils/test_files/variants/bnd.base.vcf.gz", "comp": "/Users/english/code/truvari/repo_utils/test_files/variants/bnd.comp2.vcf.gz", "output": "test_results/bench_bnd_decomp/", "includebed": null, "extend": 0, "debug": false, "reference": null, "refdist": 500, "pctseq": 0.0, "pctsize": 0.7, "pctovl": 0.0, "typeignore": false, "no_roll": true, "chunksize": 1000, "bSample": "HG008-T", "cSample": "HG008_NP_PB_germline", "dup_to_ins": false, "bnddist": 100, "sizemin": 50, "sizefilt": 30, "sizemax": 1000000000, "passonly": false, "no_ref": false, "pick": "multi", "ignore_monref": true, "check_multi": true, "check_monref": true, "no_single_bnd": true, "write_resolved": false, "decompose": true, "short_circuit": false, "skip_gt": false} \ No newline at end of file diff --git a/repo_utils/answer_key/bench/bench_bnd_decomp/summary.json b/repo_utils/answer_key/bench/bench_bnd_decomp/summary.json new file mode 100644 index 00000000..5b692f0c --- /dev/null +++ b/repo_utils/answer_key/bench/bench_bnd_decomp/summary.json @@ -0,0 +1,25 @@ +{ + "TP-base": 137, + "TP-comp": 129, + "FP": 28401, + "FN": 33, + "precision": 0.00452155625657203, + "recall": 0.8058823529411765, + "f1": 0.0089926574974431, + "base cnt": 170, + "comp cnt": 28530, + "TP-comp_TP-gt": 1, + "TP-comp_FP-gt": 128, + "TP-base_TP-gt": 1, + "TP-base_FP-gt": 136, + "gt_concordance": 0.007751937984496124, + "gt_matrix": { + "(0, 1)": { + "(0, 0)": 134, + "(0, 1)": 1 + }, + "(1, 0)": { + "(0, 0)": 2 + } + } +} \ No newline at end of file diff --git a/repo_utils/answer_key/bench/bench_bnd_decomp/tp-base.vcf.gz b/repo_utils/answer_key/bench/bench_bnd_decomp/tp-base.vcf.gz new file mode 100644 index 00000000..20fbc23a Binary files /dev/null and b/repo_utils/answer_key/bench/bench_bnd_decomp/tp-base.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_bnd_decomp/tp-base.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_bnd_decomp/tp-base.vcf.gz.tbi new file mode 100644 index 00000000..1eaaba64 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_bnd_decomp/tp-base.vcf.gz.tbi differ diff --git a/repo_utils/answer_key/bench/bench_bnd_decomp/tp-comp.vcf.gz b/repo_utils/answer_key/bench/bench_bnd_decomp/tp-comp.vcf.gz new file mode 100644 index 00000000..ebcb701d Binary files /dev/null and b/repo_utils/answer_key/bench/bench_bnd_decomp/tp-comp.vcf.gz differ diff --git a/repo_utils/answer_key/bench/bench_bnd_decomp/tp-comp.vcf.gz.tbi b/repo_utils/answer_key/bench/bench_bnd_decomp/tp-comp.vcf.gz.tbi new file mode 100644 index 00000000..a4595605 Binary files /dev/null and b/repo_utils/answer_key/bench/bench_bnd_decomp/tp-comp.vcf.gz.tbi differ diff --git a/repo_utils/sub_tests/bench.sh b/repo_utils/sub_tests/bench.sh index a6adb208..2179f056 100644 --- a/repo_utils/sub_tests/bench.sh +++ b/repo_utils/sub_tests/bench.sh @@ -75,7 +75,7 @@ run bench_gtcomp_edgecase1 $truv bench -b $INDIR/variants/gtcomp_problem1_base.v if [ $bench_gtcomp_edgecase1 ]; then bench_assert _gtcomp_edgecase1 fi -run bench_badparams $truv bench -b nofile.vcf -c nofile.aga -f notref.fa -o $OD +run bench_badparams $truv bench -b nofile.vcf -c nofile.aga -f notref.fa -o $OD --refdist 0 --extend if [ $bench_badparams ]; then assert_exit_code 100 fi @@ -89,7 +89,15 @@ fi run bench_bnd $truv bench -b $INDIR/variants/bnd.base.vcf.gz \ -c $INDIR/variants/bnd.comp.vcf.gz \ - -p 0 -o $OD/bench_bnd/ --debug + -p 0 -o $OD/bench_bnd/ --no-decompose if [ $bench_bnd ]; then bench_assert _bnd fi + +run bench_bnd_decomp $truv bench -b $INDIR/variants/bnd.base.vcf.gz \ + -c $INDIR/variants/bnd.comp2.vcf.gz \ + --sizemax 1000000000 -p 0 --pick multi \ + -o $OD/bench_bnd_decomp/ +if [ $bench_bnd_decomp ]; then + bench_assert _bnd_decomp/ +fi diff --git a/repo_utils/test_files/variants/bnd.comp2.vcf.gz b/repo_utils/test_files/variants/bnd.comp2.vcf.gz new file mode 100644 index 00000000..ded1e185 Binary files /dev/null and b/repo_utils/test_files/variants/bnd.comp2.vcf.gz differ diff --git a/repo_utils/test_files/variants/bnd.comp2.vcf.gz.tbi b/repo_utils/test_files/variants/bnd.comp2.vcf.gz.tbi new file mode 100644 index 00000000..ac6864e9 Binary files /dev/null and b/repo_utils/test_files/variants/bnd.comp2.vcf.gz.tbi differ diff --git a/truvari/bench.py b/truvari/bench.py index 01ef2f11..304611be 100644 --- a/truvari/bench.py +++ b/truvari/bench.py @@ -64,6 +64,8 @@ def parse_args(args): help="Maximum distance allowed between BNDs (%(default)s; -1=off)") thresg.add_argument("-C", "--chunksize", type=truvari.restricted_int, default=defaults.chunksize, help="Max reference distance to compare calls (%(default)s)") + thresg.add_argument("--no-decompose", action="store_false", + help="Disallow symbolic variant decomposition to BNDs") genoty = parser.add_argument_group("Genotype Comparison Arguments") genoty.add_argument("--bSample", type=str, default=None, @@ -766,7 +768,7 @@ def bench_main(cmdargs): sys.stderr.write("Couldn't run Truvari. Please fix parameters\n") sys.exit(100) - params = truvari.VariantParams(args, short_circuit=args.short) + params = truvari.VariantParams(args, short_circuit=args.short, decompose=args.no_decompose) m_bench = Bench(params=params, base_vcf=args.base, diff --git a/truvari/variant_params.py b/truvari/variant_params.py index 2ec9180a..e3ed9aa0 100644 --- a/truvari/variant_params.py +++ b/truvari/variant_params.py @@ -57,6 +57,8 @@ class VariantParams(): - Whether to exclude single-end breakends (BNDs) from comparisons. Default: `True`. * - `write_resolved` - Whether to write resolved REF/ALT sequences to output. Default: `False`. + * - `decompose` + - Decompose symbolic variants (e.g. ) into BNDs when comparing with BNDs. Default: `True` * - `short_circuit` - Whether to enable short-circuit logic for early exits in comparisons. Default: `False`. * - `skip_gt` @@ -88,6 +90,7 @@ class VariantParams(): "check_monref": True, "no_single_bnd": True, "write_resolved": False, + "decompose": True, "short_circuit": False, "skip_gt": False, } diff --git a/truvari/variant_record.py b/truvari/variant_record.py index a96bcaa0..a7a43396 100644 --- a/truvari/variant_record.py +++ b/truvari/variant_record.py @@ -10,7 +10,7 @@ RC = str.maketrans("ATCG", "TAGC") - +# pylint: disable=access-member-before-definition, attribute-defined-outside-init class VariantRecord: """ Wrapper around pysam.VariantRecords with helper functions of variant properties and basic comparisons @@ -24,6 +24,7 @@ def __init__(self, record, params=None): self.resolved_ref = None self.resolved_alt = None self.end = record.stop + self.decomp_repr = None if params is None: self.params = truvari.VariantParams() else: @@ -291,14 +292,17 @@ def decompose(self): """ Decompose symbolic DEL, DUP, and INV variants into BNDs Returns a list of new BND variant records + Stores decomposed variants in self.decomposed """ if not self.is_symbolic(): raise ValueError("Can only decompose symbolic variants") - + if self.decomp_repr: + return self.decomp_repr svtype = self.var_type() chrom = self.chrom pos = self.pos end = self.end + ret = [] if svtype == truvari.SV.INV: record1 = self.copy() record1.alts = (f"[{chrom}:{end}[N",) @@ -318,9 +322,9 @@ def decompose(self): record4.alts = (f"[{chrom}:{pos}[N",) record4.info["SVTYPE"] = "BND" - return [record1, record2, record3, record4] + ret = [record1, record2, record3, record4] - if svtype == truvari.SV.DEL: + elif svtype == truvari.SV.DEL: record1 = self.copy() record1.alts = (f"N]chr{chrom}:{end}]",) record1.info["SVTYPE"] = "BND" @@ -330,9 +334,9 @@ def decompose(self): record2.alts = (f"[chr{chrom}:{pos}[N",) record2.info["SVTYPE"] = "BND" - return [record1, record2] + ret = [record1, record2] - if svtype == truvari.SV.DUP: + elif svtype == truvari.SV.DUP: record1 = self.copy() record1.alts = (f"N]chr{chrom}:{end}]",) record1.info["SVTYPE"] = "BND" @@ -342,9 +346,9 @@ def decompose(self): record2.alts = (f"[chr{chrom}:{pos}[N",) record2.info["SVTYPE"] = "BND" - return [record1, record2] - - return [] + ret = [record1, record2] + self.decomp_repr = ret + return ret def distance(self, other): """ @@ -567,7 +571,8 @@ def match(self, other): return self.var_match(other) if self.is_bnd() and other.is_bnd(): return self.bnd_match(other) - if (self.is_symbolic() and other.is_bnd()) or (self.is_bnd() and other.is_symbolic()): + if self.params.decompose and ((self.is_symbolic() and other.is_bnd()) \ + or (self.is_bnd() and other.is_symbolic())): return self.cpx_match(other) mat = truvari.MatchResult() mat.base = self