fix no EVIDENCE bug in stitch_fragmented_CNVs.sh (#818) #821
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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.
xiaoli0
changed the title
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Thanks for contributing! Per my response to #818, this change will require extensive testing, and we expect defragment_cnvs.py is making up for this, so we may not be able to prioritize this right away. |
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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.