Filter SNPs in multiple-sample vcf based on the snps of two samples

Question

[QPaps04]

Hello all,

I have a .vcf file with ~96 samples which were called using freebayes.

This .vcf file contains a family, i.e. a mother, father and offspring. I would like to filter the SNPs of the offspring based on the parental polymorphisms (those found in the mother and father).

Is there a relatively simple way to do this? I am very new to SNP filtering and .vcf files.

Thank you in advance for your help! Eve

[QPaps04]

thank you both for your suggestions :D

Answer 1

[JC]

Check Gemini to pedigree analysis.

Answer 2

[Pierre Lindenbaum]

use

bcftools view with option '-i' (see manual)

use gatk SelectVariants with a jexl expression https://gatk.broadinstitute.org/hc/en-us/articles/360036362532-SelectVariants

use jvarkit http://lindenb.github.io/jvarkit/VcfFilterJdk.html