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nf-core / sarek

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
https://nf-co.re/sarek
MIT License
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Intersection of VCF-files #809

Open asp8200 opened 1 year ago

asp8200 commented 1 year ago

Description of feature

Some users requested that Sarek produce a VCF-file which is the "intersection" of the VCF-files from the different variant-callers. Additional description can be found here:

https://nfcore.slack.com/archives/CGFUX04HZ/p1667579492003829

@adamrtalbot and @drpatelh suggest using bcftools isec for this.

This is somewhat similar to the following issue which we plan to solve using bcftools concat: https://github.com/nf-core/sarek/issues/738

FriederikeHanssen commented 1 year ago

worked on in PR #792

asp8200 commented 1 year ago

worked on in PR #792

@FriederikeHanssen : Well, I'm not sure about that 🤔 In #792 I'm using bfctools concat and in this issue #809 we want to use bcftools isec, but first solving #792 should make it easier to solve #809 which is a very similar issue.

FriederikeHanssen commented 1 year ago

Ah my bad I thought the two are in the same PR. Then maybe jus un-assign yourself 🙂