Compare 2 VCF files A & B and return TRUE for every A variant in B, FALSE otherwise

Question

[felixm]

Hello,

My problem is I think simple.

I have 2 VCF files: A.vcf and B.vcf

A.vcf has 300,000 variants.

B.vcf has 3,000,000 variants.

I would like to compare A.vcf and B.vcf and return a boolean (TRUE/FALSE, 1/0) vector of length 300,000.

The vector should have TRUE if the entry of A is also in B. FALSE otherwise.

How can I achieve this please?

Best regards,

Felix

[Pierre Lindenbaum]

have a look at bcftools isec