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
Checking kinship coefficients and relationships and comparing genotyping data to exomes
Question: Obtaining list of / manually specifying interrogation sites in Peddy
Obtaining list of / manually specifying interrogation sites in Peddy
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gaelgarcia
1 answer
Check for Mendel errors, and be suspicious of any sample with a large number of them. “plink —mendel” is one way to do this.
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