Filter SNPs in multiple-sample vcf based on the snps of two samples
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4.9 years ago
QPaps04 ▴ 160

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

vcf SNP filter bash linux • 1.4k views
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thank you both for your suggestions :D

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4.9 years ago
JC 13k

Check Gemini to pedigree analysis.

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4.9 years ago

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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