Annotate single sample output with gnomAD allele frequencies and add …

…BED output (#40) * add external af annotation to module07 wdl * modify annotation scripts to not fail if given empty file * produce bed files as additional single sample output * add external af annotation inputs to jsons * update sv-pipeline docker
broadinstitute · Sep 9, 2020 · 105a9e0 · 105a9e0
1 parent 2eda0da
commit 105a9e0
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Showing 44 changed files with 163 additions and 53 deletions.
diff --git a/inputs/GATKSVPipelineBatch.ref_panel_1kg.json b/inputs/GATKSVPipelineBatch.ref_panel_1kg.json
@@ -782,7 +782,7 @@
   "GATKSVPipelineBatch.sv_base_docker": "gatksv/sv-base:b3af2e3",
   "GATKSVPipelineBatch.sv_pipeline_base_docker": "gatksv/sv-pipeline-base:b3af2e3",
   "GATKSVPipelineBatch.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "GATKSVPipelineBatch.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "GATKSVPipelineBatch.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "GATKSVPipelineBatch.sv_pipeline_qc_docker": "epiercehoffman/sv-pipeline-qc:eph_03qc_variables-e597d85",
   "GATKSVPipelineBatch.sv_pipeline_rdtest_docker": "gatksv/sv-pipeline-rdtest:b3af2e3",
   "GATKSVPipelineBatch.samtools_cloud_docker": "gatksv/samtools-cloud:b3af2e3",

diff --git a/inputs/GATKSVPipelineSingleSample.ref_panel_1kg.na12878.json b/inputs/GATKSVPipelineSingleSample.ref_panel_1kg.na12878.json
@@ -33,7 +33,7 @@
   "GATKSVPipelineSingleSample.sv_base_docker": "gatksv/sv-base:b3af2e3",
   "GATKSVPipelineSingleSample.sv_pipeline_base_docker": "gatksv/sv-pipeline-base:b3af2e3",
   "GATKSVPipelineSingleSample.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "GATKSVPipelineSingleSample.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "GATKSVPipelineSingleSample.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "GATKSVPipelineSingleSample.sv_pipeline_qc_docker": "epiercehoffman/sv-pipeline-qc:eph_03qc_variables-e597d85",
   "GATKSVPipelineSingleSample.sv_pipeline_rdtest_docker": "gatksv/sv-pipeline-rdtest:b3af2e3",
   "GATKSVPipelineSingleSample.wham_docker": "gatksv/wham:8645aa",
@@ -92,6 +92,10 @@
   "GATKSVPipelineSingleSample.linc_rna_gtf" :       "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/gencode.lincRNA.gtf.gz",
   "GATKSVPipelineSingleSample.promoter_bed" :       "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/promoter.bed",
   "GATKSVPipelineSingleSample.noncoding_bed" :       "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/noncoding.sort.hg38.bed",
+  "GATKSVPipelineSingleSample.external_af_ref_bed" :       "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/gnomad_AF/gnomad_v2.1_sv.sites.GRCh38.bed.gz",
+  "GATKSVPipelineSingleSample.external_af_ref_bed_prefix" :       "gnomad_v2.1_sv",
+  "GATKSVPipelineSingleSample.external_af_population" :      ["ALL", "AFR", "AMR", "EAS", "EUR"],
+
   "GATKSVPipelineSingleSample.annotation_sv_per_shard" : "5000",
 
   "GATKSVPipelineSingleSample.cnmops_mem_gb_override_sample3": 24,

diff --git a/inputs/GATKSVPipelineSingleSample.ref_panel_1kg.na12878.no_melt.json b/inputs/GATKSVPipelineSingleSample.ref_panel_1kg.na12878.no_melt.json
@@ -34,7 +34,7 @@
   "GATKSVPipelineSingleSample.sv_base_docker": "gatksv/sv-base:b3af2e3",
   "GATKSVPipelineSingleSample.sv_pipeline_base_docker": "gatksv/sv-pipeline-base:b3af2e3",
   "GATKSVPipelineSingleSample.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "GATKSVPipelineSingleSample.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "GATKSVPipelineSingleSample.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "GATKSVPipelineSingleSample.sv_pipeline_qc_docker": "epiercehoffman/sv-pipeline-qc:eph_03qc_variables-e597d85",
   "GATKSVPipelineSingleSample.sv_pipeline_rdtest_docker": "gatksv/sv-pipeline-rdtest:b3af2e3",
   "GATKSVPipelineSingleSample.wham_docker": "gatksv/wham:8645aa",
@@ -92,6 +92,10 @@
   "GATKSVPipelineSingleSample.linc_rna_gtf" :       "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/gencode.lincRNA.gtf.gz",
   "GATKSVPipelineSingleSample.promoter_bed" :       "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/promoter.bed",
   "GATKSVPipelineSingleSample.noncoding_bed" :       "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/noncoding.sort.hg38.bed",
+  "GATKSVPipelineSingleSample.external_af_ref_bed" :       "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/gnomad_AF/gnomad_v2.1_sv.sites.GRCh38.bed.gz",
+  "GATKSVPipelineSingleSample.external_af_ref_bed_prefix" :       "gnomad_v2.1_sv",
+  "GATKSVPipelineSingleSample.external_af_population" :      ["ALL", "AFR", "AMR", "EAS", "EUR"],
+
   "GATKSVPipelineSingleSample.annotation_sv_per_shard" : "5000",
 
   "GATKSVPipelineSingleSample.cnmops_mem_gb_override_sample3": 24,

diff --git a/src/sv-pipeline/05_annotation/scripts/R1.bedtools_closest_CNV.R b/src/sv-pipeline/05_annotation/scripts/R1.bedtools_closest_CNV.R
@@ -106,7 +106,23 @@ add_SV_Size<-function(chs){
   return(chs)
 	}
 
+pop=read.table(pop_file)
+pop_colname = paste(pop[,1],'AF',sep='_')
+pop_colname[pop_colname=='ALL_AF']='AF'
+
+out_columns <- c('name','name.1',pop_colname,'Reciprocal_Overlap')
+
 dat=read.table(input_bed,sep='\t', header=T)
+# if there's no data write an empty table and exit
+if (nrow(dat) == 0) {
+	out_columns[c(1,2)]=c('query_svid','ref_svid')
+	out2 <- data.frame(matrix(ncol = length(out_columns), nrow = 0))
+	names(out2) <- out_columns
+	write.table(out2, output_bed, quote=F, sep='\t', col.names=T, row.names=F)
+	quit()
+}
+
+
 dat[,ncol(dat)+1] = apply(dat,1,function(x){return(max(c(as.integer(x[2]), as.integer(x[8]))))})
 dat[,ncol(dat)+1] = apply(dat,1,function(x){return(min(c(as.integer(x[3]), as.integer(x[9]))))})
 dat[,ncol(dat)+1] = dat[,ncol(dat)]-dat[,ncol(dat)-1]
@@ -128,11 +144,7 @@ out=out[order(out[,2]),]
 out=out[order(out[,1]),]
 colnames(out)[ncol(out)]='Reciprocal_Overlap'
 
-pop=read.table(pop_file)
-pop_colname = paste(pop[,1],'AF',sep='_')
-pop_colname[pop_colname=='ALL_AF']='AF'
-
-out2 = out[,c('name','name.1',pop_colname,'Reciprocal_Overlap')]
+out2 = out[,out_columns]
 colnames(out2)[c(1,2)]=c('query_svid','ref_svid')
 out2=out2[out2$Reciprocal_Overlap>.5,]
 write.table(out2, output_bed, quote=F, sep='\t', col.names=T, row.names=F)

diff --git a/src/sv-pipeline/05_annotation/scripts/R2.bedtools_closest_INS.R b/src/sv-pipeline/05_annotation/scripts/R2.bedtools_closest_INS.R
@@ -106,7 +106,22 @@ add_SV_Size<-function(chs){
   return(chs)
 	}
 
+pop=read.table(pop_file)
+pop_colname = paste(pop[,1],'AF',sep='_')
+pop_colname[pop_colname=='ALL_AF']='AF'
+
+out_columns <- c('name','name.1',pop_colname,'INS_dis','INS_ratio')
+
 dat=read.table(input_bed,sep='\t', header=T)
+# if there's no data write an empty table and exit
+if (nrow(dat) == 0) {
+	out_columns[c(1,2)]=c('query_svid','ref_svid')
+	out2 <- data.frame(matrix(ncol = length(out_columns), nrow = 0))
+	names(out2) <- out_columns
+	write.table(out2, output_bed, quote=F, sep='\t', col.names=T, row.names=F)
+	quit()
+}
+
 dat[,ncol(dat)+1] =abs(dat[,8]-dat[,2])
 colnames(dat)[ncol(dat)]='INS_dis'
 dat[,ncol(dat)+1] = dat[,13]/dat[,6]
@@ -127,11 +142,7 @@ out=out[order(out[,3]),]
 out=out[order(out[,2]),]
 out=out[order(out[,1]),]
 
-pop=read.table(pop_file)
-pop_colname = paste(pop[,1],'AF',sep='_')
-pop_colname[pop_colname=='ALL_AF']='AF'
-
-out2 = out[,c('name','name.1',pop_colname,'INS_dis','INS_ratio')]
+out2 = out[,out_columns]
 colnames(out2)[c(1,2)]=c('query_svid','ref_svid')
 
 out2=out2[out2$INS_dis<100 & out2$INS_ratio<10 & out2$INS_ratio>.1,]

diff --git a/test/batch/GATKSVPipelineBatch.test_large.json b/test/batch/GATKSVPipelineBatch.test_large.json
@@ -350,7 +350,7 @@
   "GATKSVPipelineBatch.sv_base_docker": "gatksv/sv-base:b3af2e3",
   "GATKSVPipelineBatch.sv_pipeline_base_docker": "gatksv/sv-pipeline-base:b3af2e3",
   "GATKSVPipelineBatch.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "GATKSVPipelineBatch.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "GATKSVPipelineBatch.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "GATKSVPipelineBatch.sv_pipeline_qc_docker": "epiercehoffman/sv-pipeline-qc:eph_03qc_variables-e597d85",
   "GATKSVPipelineBatch.sv_pipeline_rdtest_docker": "gatksv/sv-pipeline-rdtest:b3af2e3",
   "GATKSVPipelineBatch.wham_docker": "gatksv/wham:8645aa",

diff --git a/test/module00a/Module00aBatch.test_large.json b/test/module00a/Module00aBatch.test_large.json
@@ -18,7 +18,7 @@
 
   "Module00aBatch.samtools_cloud_docker": "gatksv/samtools-cloud:b3af2e3",
   "Module00aBatch.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module00aBatch.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module00aBatch.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module00aBatch.delly_docker": "gatksv/delly:8645aa",
   "Module00aBatch.manta_docker": "gatksv/manta:8645aa",
   "Module00aBatch.melt_docker" : "us.gcr.io/talkowski-sv-gnomad/melt:8645aa",

diff --git a/test/module00a/Module00aBatch.test_small.json b/test/module00a/Module00aBatch.test_small.json
@@ -18,7 +18,7 @@
 
   "Module00aBatch.samtools_cloud_docker": "gatksv/samtools-cloud:b3af2e3",
   "Module00aBatch.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module00aBatch.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module00aBatch.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module00aBatch.manta_docker": "gatksv/manta:8645aa",
   "Module00aBatch.melt_docker" : "us.gcr.io/talkowski-sv-gnomad/melt:8645aa",
   "Module00aBatch.wham_docker": "gatksv/wham:8645aa",

diff --git a/test/module00a/Module00aBatchTest.test_large.json b/test/module00a/Module00aBatchTest.test_large.json
@@ -454,7 +454,7 @@
 
   "Module00aBatchTest.Module00aBatch.samtools_cloud_docker": "gatksv/samtools-cloud:b3af2e3",
   "Module00aBatchTest.Module00aBatch.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module00aBatchTest.Module00aBatch.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module00aBatchTest.Module00aBatch.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module00aBatchTest.Module00aBatch.delly_docker": "gatksv/delly:8645aa",
   "Module00aBatchTest.Module00aBatch.manta_docker": "gatksv/manta:8645aa",
   "Module00aBatchTest.Module00aBatch.melt_docker" : "us.gcr.io/talkowski-sv-gnomad/melt:8645aa",

diff --git a/test/module00a/Module00aBatchTest.test_small.json b/test/module00a/Module00aBatchTest.test_small.json
@@ -75,7 +75,7 @@
 
   "Module00aBatchTest.Module00aBatch.samtools_cloud_docker": "gatksv/samtools-cloud:b3af2e3",
   "Module00aBatchTest.Module00aBatch.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module00aBatchTest.Module00aBatch.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module00aBatchTest.Module00aBatch.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module00aBatchTest.Module00aBatch.manta_docker": "gatksv/manta:8645aa",
   "Module00aBatchTest.Module00aBatch.melt_docker" : "us.gcr.io/talkowski-sv-gnomad/melt:8645aa",
   "Module00aBatchTest.Module00aBatch.wham_docker": "gatksv/wham:8645aa",

diff --git a/test/module00b/Module00b.test_large.json b/test/module00b/Module00b.test_large.json
@@ -1,7 +1,7 @@
 {
   "Module00b.run_vcf_qc" : "true",
   "Module00b.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module00b.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module00b.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module00b.sv_pipeline_qc_docker": "epiercehoffman/sv-pipeline-qc:eph_03qc_variables-e597d85",
   "Module00b.wgd_scoring_mask": "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/wgd_scoring_mask.hg38.gnomad_v3.bed",
   "Module00b.genome_file": "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/hg38.genome",

diff --git a/test/module00b/Module00b.test_small.json b/test/module00b/Module00b.test_small.json
@@ -1,7 +1,7 @@
 {
   "Module00b.run_vcf_qc" : "true",
   "Module00b.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module00b.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module00b.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module00b.sv_pipeline_qc_docker": "epiercehoffman/sv-pipeline-qc:eph_03qc_variables-e597d85",
   "Module00b.wgd_scoring_mask": "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/wgd_scoring_mask.hg38.gnomad_v3.bed",
   "Module00b.genome_file": "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/hg38.genome",

diff --git a/test/module00c/Module00c.test_large.json b/test/module00c/Module00c.test_large.json
@@ -1,6 +1,6 @@
 {
   "Module00c.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module00c.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module00c.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module00c.sv_pipeline_qc_docker": "epiercehoffman/sv-pipeline-qc:eph_03qc_variables-e597d85",
   "Module00c.cnmops_docker": "gatksv/cnmops:b3af2e3",
   "Module00c.linux_docker" : "ubuntu:18.04",

diff --git a/test/module00c/Module00c.test_small.json b/test/module00c/Module00c.test_small.json
@@ -1,6 +1,6 @@
 {
   "Module00c.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module00c.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module00c.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module00c.sv_pipeline_qc_docker": "epiercehoffman/sv-pipeline-qc:eph_03qc_variables-e597d85",
   "Module00c.cnmops_docker": "gatksv/cnmops:b3af2e3",
   "Module00c.linux_docker" : "ubuntu:18.04",

diff --git a/test/module00c/Module00cTest.test_baf_from_vcf.json b/test/module00c/Module00cTest.test_baf_from_vcf.json
@@ -440,7 +440,7 @@
   ],
 
   "Module00cTest.Module00c.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module00cTest.Module00c.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module00cTest.Module00c.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module00cTest.Module00c.sv_pipeline_qc_docker": "epiercehoffman/sv-pipeline-qc:eph_03qc_variables-e597d85",
   "Module00cTest.Module00c.cnmops_docker": "gatksv/cnmops:b3af2e3",
   "Module00cTest.Module00c.linux_docker" : "ubuntu:18.04",

diff --git a/test/module00c/Module00cTest.test_large.json b/test/module00c/Module00cTest.test_large.json
@@ -440,7 +440,7 @@
   ],
 
   "Module00cTest.Module00c.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module00cTest.Module00c.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module00cTest.Module00c.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module00cTest.Module00c.sv_pipeline_qc_docker": "epiercehoffman/sv-pipeline-qc:eph_03qc_variables-e597d85",
   "Module00cTest.Module00c.cnmops_docker": "gatksv/cnmops:b3af2e3",
   "Module00cTest.Module00c.linux_docker" : "ubuntu:18.04",

diff --git a/test/module00c/Module00cTest.test_small.json b/test/module00c/Module00cTest.test_small.json
@@ -60,7 +60,7 @@
   ],
 
   "Module00cTest.Module00c.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module00cTest.Module00c.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module00cTest.Module00c.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module00cTest.Module00c.sv_pipeline_qc_docker": "epiercehoffman/sv-pipeline-qc:eph_03qc_variables-e597d85",
   "Module00cTest.Module00c.cnmops_docker": "gatksv/cnmops:b3af2e3",
   "Module00cTest.Module00c.linux_docker" : "ubuntu:18.04",

diff --git a/test/module01/Module01.test_large.json b/test/module01/Module01.test_large.json
@@ -1,6 +1,6 @@
 {
   "Module01.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module01.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module01.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
 
   "Module01.contigs": "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/contig.fai",
   "Module01.depth_flags": "--merge-coordinates",

diff --git a/test/module01/Module01.test_small.json b/test/module01/Module01.test_small.json
@@ -1,6 +1,6 @@
 {
   "Module01.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module01.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module01.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
 
   "Module01.contigs": "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/contig.fai",
   "Module01.depth_flags": "--merge-coordinates",

diff --git a/test/module01/Module01Test.test_large.json b/test/module01/Module01Test.test_large.json
@@ -125,7 +125,7 @@
   "Module01Test.Module01Metrics.Module01Metrics.wham_metrics.mem_gib" : 3.75,
 
   "Module01Test.Module01.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module01Test.Module01.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module01Test.Module01.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
 
   "Module01Test.Module01.contigs": "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/contig.fai",
   "Module01Test.Module01.depth_flags": "--merge-coordinates",

diff --git a/test/module01/Module01Test.test_small.json b/test/module01/Module01Test.test_small.json
@@ -25,7 +25,7 @@
   "Module01Test.Module01Metrics.baseline_melt_vcf" : "gs://gatk-sv-resources/test/module01/small/output/test_small.melt.vcf.gz",
 
   "Module01Test.Module01.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module01Test.Module01.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module01Test.Module01.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
 
   "Module01Test.Module01.contigs": "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/contig.fai",
   "Module01Test.Module01.depth_flags": "--merge-coordinates",

diff --git a/test/module02/Module02.test_large.json b/test/module02/Module02.test_large.json
@@ -1,5 +1,5 @@
 {
-  "Module02.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module02.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module02.sv_pipeline_rdtest_docker": "gatksv/sv-pipeline-rdtest:b3af2e3",
   "Module02.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
   "Module02.sv_base_docker": "gatksv/sv-base:b3af2e3",

diff --git a/test/module02/Module02.test_small.json b/test/module02/Module02.test_small.json
@@ -1,5 +1,5 @@
 {
-  "Module02.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module02.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module02.sv_pipeline_rdtest_docker": "gatksv/sv-pipeline-rdtest:b3af2e3",
   "Module02.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
   "Module02.sv_base_docker": "gatksv/sv-base:b3af2e3",

diff --git a/test/module02/Module02Test.test_large.json b/test/module02/Module02Test.test_large.json
@@ -114,7 +114,7 @@
   "Module02Test.Module02Metrics.linux_docker" : "ubuntu:18.04",
   "Module02Test.Module02Metrics.contig_list" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/primary_contigs.list",
 
-  "Module02Test.Module02.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module02Test.Module02.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module02Test.Module02.sv_pipeline_rdtest_docker": "gatksv/sv-pipeline-rdtest:b3af2e3",
   "Module02Test.Module02.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
   "Module02Test.Module02.sv_base_docker": "gatksv/sv-base:b3af2e3",

diff --git a/test/module02/Module02Test.test_small.json b/test/module02/Module02Test.test_small.json
@@ -19,7 +19,7 @@
   "Module02Test.Module02Metrics.linux_docker" : "ubuntu:18.04",
   "Module02Test.Module02Metrics.contig_list" : "gs://gcp-public-data--broad-references/hg38/v0/sv-resources/resources/v1/primary_contigs.list",
 
-  "Module02Test.Module02.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module02Test.Module02.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module02Test.Module02.sv_pipeline_rdtest_docker": "gatksv/sv-pipeline-rdtest:b3af2e3",
   "Module02Test.Module02.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
   "Module02Test.Module02.sv_base_docker": "gatksv/sv-base:b3af2e3",

diff --git a/test/module03/Module03.test_large.json b/test/module03/Module03.test_large.json
@@ -1,5 +1,5 @@
 {
-  "Module03.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module03.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module03.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
   "Module03.linux_docker" : "ubuntu:18.04",
 

diff --git a/test/module03/Module03Qc.test_large.json b/test/module03/Module03Qc.test_large.json
@@ -25,7 +25,7 @@
   "Module03Qc.werling_2018_tarball": "gs://gatk-sv-resources-secure/resources/Werling_2018_hg38.tar.gz",
 
 
-  "Module03Qc.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module03Qc.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module03Qc.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
   "Module03Qc.sv_pipeline_qc_docker": "epiercehoffman/sv-pipeline-qc:eph_03qc_variables-e597d85",
 

diff --git a/test/module03/Module03Test.test_large.json b/test/module03/Module03Test.test_large.json
@@ -120,7 +120,7 @@
   "Module03Test.Module03Metrics.Module03Metrics.PESR_VCF_Metrics.mem_gib" : "3.75",
   "Module03Test.Module03Metrics.Module03Metrics.Depth_VCF_Metrics.mem_gib" : "1.5",
 
-  "Module03Test.Module03.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module03Test.Module03.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module03Test.Module03.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
   "Module03Test.Module03.linux_docker" : "ubuntu:18.04",
 

diff --git a/test/module04/MergeCohortVcfs.test.json b/test/module04/MergeCohortVcfs.test.json
@@ -1,5 +1,5 @@
 {
-  "MergeCohortVcfs.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "MergeCohortVcfs.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "MergeCohortVcfs.pesr_vcfs": ["gs://gatk-sv-resources/test/module03/large/output/test_large.filtered_pesr_merged.vcf.gz"],
   "MergeCohortVcfs.depth_vcfs": ["gs://gatk-sv-resources/test/module03/large/output/test_large.depth.outliers_removed.vcf.gz"]
 }
diff --git a/test/module04/Module04.test_large.json b/test/module04/Module04.test_large.json
@@ -1,6 +1,6 @@
 {
   "Module04.sv_base_mini_docker": "gatksv/sv-base-mini:b3af2e3",
-  "Module04.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_single_sample_ctx_rep_eccc9be",
+  "Module04.sv_pipeline_docker": "cwhelan/sv-pipeline:cw_external_af_annotation_565a1e",
   "Module04.sv_pipeline_rdtest_docker": "gatksv/sv-pipeline-rdtest:b3af2e3",
   "Module04.linux_docker" : "ubuntu:18.04",