Tools to check consistency between VCF genotypes and pedigree-stated sex and family relationships

Question

[gaelgarcia]

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

[WouterDeCoster]

Tagging brentp

Answer 1

[chrchang523]

Check for Mendel errors, and be suspicious of any sample with a large number of them. “plink —mendel” is one way to do this.