Find SNPs common to mutants, absent in WT (vcf files)

Question

[charlesh]

Hi,

I have 3 vcf files from WT and mut1, mut2 I would like to get a file with an intersection of common SNPs to the 2 Mutants, but absent from the WT sample.

I've run bcftools isec on all pairs of samples, but am hung up on using the resulting 3 sets of vcf files (0000, 00011,0002,0003) to identify SNPs common to the mutants, but absent from the WT.

Suggestions? Charles

[Pierre Lindenbaum]

merge the 3 vcf files with bcftools and select the variants with gatk SelectVariants --select <expr> https://gatk.broadinstitute.org/hc/en-us/articles/360036726131-SelectVariants