extract SNPs present only in one individual and not in all the others from a multisample vcf file

Question

[elena.paesini]

Hi, I have a multi-samples vcf file with four samples. I want to extract the variants present only in one specific individual but not present in the others 3 individuals. Namely, I want to extract the variants which are typical of that individual. Which is the simplest way to do this? Thanks

Answer 1

[Kevin Blighe]

To identify samples that are 'private' to a specific sample, then use:

bcftools view --private --samples 2624 MyVariants.vcf

Here, sample 2624 is the sample for whom I want to identify private variants.

Kevin