How to merge VCF from disjoint sample lists · Biostar

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How to merge VCF from disjoint sample lists

Hi All, I am trying to merge VCF files from two different cohorts. Since one cohort is smaller in size, there are a different number of variants between these VCF files. Can you please suggest me the tools/commands that merge these VCF files? Note: if there are samples with no variants in one or the other cohorts, I want to have REF/REF for those samples in the merged file. Thanks!

vcf

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updated 4.3 years ago by Ram

• written 4.3 years ago by MAPK2 •

1 answer

Have you taken a look at bcftools merge? It has an option -0 to "assume genotypes at missing sites are 0/0".

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written 4.3 years ago by Ram

Thanks. This is what I need.

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written 4.3 years ago by MAPK2 •

I've moved my comment to an answer. Please accept it to mark the post as solved.

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written 4.3 years ago by Ram

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