reheader FP vcfs from full hg38 to no_alt (#344)

broadinstitute · Apr 11, 2023 · 0197e4a · 0197e4a
1 parent 5d900f1
commit 0197e4a
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Showing 3 changed files with 39 additions and 3 deletions.
diff --git a/wdl/pipelines/TechAgnostic/Utility/FindBamIdentity.wdl b/wdl/pipelines/TechAgnostic/Utility/FindBamIdentity.wdl
@@ -42,9 +42,11 @@ workflow FindBamIdentity {
     call FPUtils.PickGenotypeVCF { input: fingerprinting_vcf_gs_paths = ListGenotypedVCFs.vcf_gs_paths, vcf_name = vcf_filter_expression }
 
     scatter (vcf in PickGenotypeVCF.vcfs) {
+        call FPUtils.ReheaderFullGRCh38VCFtoNoAlt {input: full_GRCh38_vcf = vcf}
+
         call FPUtils.FilterGenotypesVCF {
             input:
-                fingerprint_vcf = vcf
+                fingerprint_vcf = ReheaderFullGRCh38VCFtoNoAlt.reheadered_vcf
         }
         call FPUtils.ExtractGenotypingSites {
             input:

diff --git a/wdl/pipelines/TechAgnostic/Utility/VerifyFingerprint.wdl b/wdl/pipelines/TechAgnostic/Utility/VerifyFingerprint.wdl
@@ -63,15 +63,16 @@ workflow VerifyFingerprint {
     }
 
     File gt_vcf = if (defined(use_this_fp_vcf)) then select_first([use_this_fp_vcf]) else select_first([PickGenotypeVCF.vcfs])[0]
+    call FPUtils.ReheaderFullGRCh38VCFtoNoAlt as reheader {input: full_GRCh38_vcf = gt_vcf}
 
     call VariantUtils.GetVCFSampleName {
         input:
-            fingerprint_vcf = gt_vcf
+            fingerprint_vcf = reheader.reheadered_vcf
     }
 
     call FPUtils.FilterGenotypesVCF {
         input:
-            fingerprint_vcf = gt_vcf
+            fingerprint_vcf = reheader.reheadered_vcf
     }
 
     call FPUtils.ExtractGenotypingSites {

diff --git a/wdl/tasks/QC/Fingerprinting.wdl b/wdl/tasks/QC/Fingerprinting.wdl
@@ -468,3 +468,36 @@ task CheckCLRFingerprint {
         docker:                select_first([runtime_attr.docker, default_attr.docker])
     }
 }
+
+task ReheaderFullGRCh38VCFtoNoAlt {
+    meta {
+        desciption:
+        "Reheader the fingperint VCF that's generated with full GRCh38 reference to the no_alt header; project specific."
+    }
+
+    input {
+        File full_GRCh38_vcf
+    }
+
+    command <<<
+        set -eux
+
+        GREPCMD="grep"
+        if [[ ~{full_GRCh38_vcf} =~ \.gz$ ]]; then
+            GREPCMD="zgrep"
+        fi
+        "${GREPCMD}" -vF "_decoy,length=" ~{full_GRCh38_vcf} | \
+            grep -vF "_alt,length=" | \
+            grep -v "^##contig=<ID=HLA-" \
+            > "reheadered.fp.vcf"
+    >>>
+
+    output {
+        File reheadered_vcf = "reheadered.fp.vcf"
+    }
+
+    runtime {
+        disks: "local-disk 100 HDD"
+        docker: "gcr.io/cloud-marketplace/google/ubuntu2004:latest"
+    }
+}