Subset WGS pVCF Permanently deleted user 13 December 2022 00:00 1 comment Is there a tool on the RAP to extract a VCF for a single (or multiple) subjects from the WGS pVCF 200k release? Comments 1 comment Sort by Date Votes Former User of DNAx Community_28 13 December 2022 19:25 There are many tools, but this is a multi-step process. Each chromosome has many segments in its pvcf file. you need to filter and concatenate across all of the segments for each chromosome. There was a discussion about that here:https://community.dnanexus.com/s/question/0D5t000003zujMJCAY/how-to-merge-vcf-files-with-swiss-army-knife Finally you will want to use bcftools for the concat and filter steps. using either the -samples or --samples-file flags All of this would be run in swiss-army-knife 0 Please sign in to leave a comment.
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There are many tools, but this is a multi-step process.
Each chromosome has many segments in its pvcf file. you need to filter and concatenate across all of the segments for each chromosome.
There was a discussion about that here:
https://community.dnanexus.com/s/question/0D5t000003zujMJCAY/how-to-merge-vcf-files-with-swiss-army-knife
Finally you will want to use bcftools for the concat and filter steps. using either the -samples or --samples-file flags
All of this would be run in swiss-army-knife
Please sign in to leave a comment.