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Old 05-03-2018, 11:13 PM   #1
friducha
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Location: UK

Join Date: Jan 2015
Posts: 9
Default Tools to check consistency between VCF genotypes & pedigree-stated sex/relationship?

X-post from Biostars.

We're currently trying to do identity checks on targeted genome sequencing data from ~15K samples. Our target panel is very specific, and only a very small fraction of the sites interrogated by Peddy are covered.

Is there a similar tool you can recommend to verify that the stated stated sex and family relationships match the relationships (relatedness, kinship, etc.) and sex inferred from a VCF?

Related:

Checking kinship coefficients and relationships and comparing genotyping data to exomes
https://www.biostars.org/p/111573/

Question: Obtaining list of / manually specifying interrogation sites in Peddy
https://www.biostars.org/p/312513/
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