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Error occurred while processing INFO tag "RPA" when use bcftools merge #2348

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TuBieJun opened this issue Dec 30, 2024 · 0 comments
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@TuBieJun
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I use follow command to merge two vcfs:

bcftools merge 41210352005326.vcf.gz.setgt.vcf.gz 41231210606008.vcf.gz.setgt.vcf.gz -o temp.vcf

Then got the error info:

[W::bcf_hdr_merge] Trying to combine "RPA" tag definitions of different lengths
Error occurred while processing INFO tag "RPA" at 1:10815

I search the position of two vcfs, found nothing strange:

$ bcftools view -H  41210352005326.vcf.gz.setgt.vcf.gz 1:10815
1       10815   rs1205319490    T       TC      103.34  PASS    AC=2;AF=1;AN=2;DP=3;Entropy=0.26;ExcessHet=3.0103;FS=0;GC=78.29;MLEAC=2;MLEAF=1;ML_PROB=0.06;MQ=39;NBQ=25.333;QD=34.45;RPA=1,2;RU=C;ReadPosEndDist=25.667;SOR=1.179;STR;UDP=4        GT:AD:DP:GQ:PL       1/1:0,3:3:9:121,9,0
 bcftools view -H  41231210606008.vcf.gz.setgt.vcf.gz 1:10815
1       10815   rs1205319490    T       TC      244.52  PASS    AC=1;AF=0.5;AN=2;BaseQRankSum=1.534;ClippingRankSum=-0;DP=10;Entropy=0.35;ExcessHet=3.0103;FS=0;GC=78.5;MLEAC=1;MLEAF=0.5;ML_PROB=0.08;MQ=43.45;MQ0=0;MQRankSum=-1.534;NBQ=28.455;QD=30.57;RPA=1,2;RU=C;ReadPosEndDist=21.5;ReadPosRankSum=-0.157;SOR=0.595;STR;UDP=10    GT:AD:DP:GQ:PL  1/1:1,7:8:21:257,0,21

The bcftools version info:

$ bcftools version
bcftools 1.20
Using htslib 1.20
Copyright (C) 2024 Genome Research Ltd.
License Expat: The MIT/Expat license
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.
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