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?
Checking kinship coefficients and relationships and comparing genotyping data to exomes
Question: Obtaining list of / manually specifying interrogation sites in Peddy