inner merge vcfs in one step?
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6 weeks ago
curious ▴ 630

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 • 212 views
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Entering edit mode
6 weeks ago
bcftools merge  -O u --file-list in.list | bcftools view -i 'COUNT(GT="hom")=0 && COUNT(GT="mis")=0' 
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