This is a test version of Biostars. For the public version, visit https://www.biostars.org.
inner merge vcfs in one step?

I have 3 vcfs with single sample each and different variants. I want one vcf with 3 samples and only variants that are present in all 3 vcfs.

I think I can do this a long way with

bcftools isec --nfiles 3 a.vcf b.vcf c.vcf

then grep out the list of variants present in all 3, do a filter step followed by standard bcftools merge

Is there any way to do this all in one step though?

bcftools
• 1,294 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by curious curious

1 answer 

bcftools merge  -O u --file-list in.list | bcftools view -i 'COUNT(GT="hom")=0 && COUNT(GT="mis")=0'
• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Log in to answer this question.

More posts like this