How do I extract certain variant from p.vcf.gz Chai Fungtammasan DNAnexus Team 15 December 2022 00:00 1 comment (question from workshop at KCL on Dec 7, 2022) Comments 1 comment Sort by Date Votes Chai Fungtammasan DNAnexus Team 15 December 2022 01:05 First, you can figure out which p.vcf.gz containing your variant. See discussion in these two forums (WES: https://community.dnanexus.com/s/question/0D5t000003u54wfCAA/for-the-chunked-population-wide-450k-wes-vcfs-where-can-one-find-a-position-file-delimiting-the-start-and-end-positions-of-each-chunk; WGS: https://community.dnanexus.com/s/question/0D5t0000048q6XmCAI/is-there-a-map-for-which-regions-are-in-each-200k-wgs-pvcf-block).Then you can use bcftools in swiss-army-knife to narrow down to variants that you want. 0 Please sign in to leave a comment.
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First, you can figure out which p.vcf.gz containing your variant. See discussion in these two forums (WES: https://community.dnanexus.com/s/question/0D5t000003u54wfCAA/for-the-chunked-population-wide-450k-wes-vcfs-where-can-one-find-a-position-file-delimiting-the-start-and-end-positions-of-each-chunk; WGS: https://community.dnanexus.com/s/question/0D5t0000048q6XmCAI/is-there-a-map-for-which-regions-are-in-each-200k-wgs-pvcf-block).
Then you can use bcftools in swiss-army-knife to narrow down to variants that you want.
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