Filter SNPs in multiple-sample vcf based on the snps of two samples
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
2 answers
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
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Pierre Lindenbaum
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thank you both for your suggestions :D