How to merge VCF from disjoint sample lists

Question

[MAPK2]

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!

Answer 1

[Ram]

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

[MAPK2]

Thanks. This is what I need.

[Ram]

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