From 9366b8d611b26e5acb1a90d92cadd86e5775c7ab Mon Sep 17 00:00:00 2001 From: zhangting1991 Date: Mon, 9 Jun 2025 09:02:57 +0800 Subject: [PATCH] fix no EVIDENCE bug in stitch_fragmented_CNVs.sh The input VCF lacks the "EVIDENCE" field in the INFO column. As a result, during the step "Subset VCF to biallelic CNVs without PE or SR support", the script will produce an empty biallelic_depth_CNVs.vcf.gz file containing no variants. This step does not raise an error or halt execution, so the pipeline continues; however, no stitched VCF is generated. Therefore, the script's output will be identical to the input. --- .../04_variant_resolution/scripts/stitch_fragmented_CNVs.sh | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/src/sv-pipeline/04_variant_resolution/scripts/stitch_fragmented_CNVs.sh b/src/sv-pipeline/04_variant_resolution/scripts/stitch_fragmented_CNVs.sh index 04128157e..56649b58b 100755 --- a/src/sv-pipeline/04_variant_resolution/scripts/stitch_fragmented_CNVs.sh +++ b/src/sv-pipeline/04_variant_resolution/scripts/stitch_fragmented_CNVs.sh @@ -96,10 +96,8 @@ zcat ${INVCF} \ | grep -e 'SVTYPE=DEL\|SVTYPE=DUP' \ | fgrep -v "MULTIALLELIC" \ | awk -v OFS="\t" '{ print $3, $8 }' \ - | sed 's/EVIDENCE=/\t/g' \ - | cut -f1,3 \ | sed 's/\;/\t/g' \ - | awk -v check=${CHECK_EVIDENCE} '{ if (check=="true" && ($2~"RD" || $2~"BAF") && $2!~"PE" && $2!~"SR") print $1 }' \ + | cut -f1 \ | fgrep -wf - <( zcat ${INVCF} ) \ | cat <( zcat ${INVCF} | fgrep "#" ) - \ | vcf-sort \