Pedigree checking from exome data

[Kath]

Hi,

Can anyone recommend a tool for checking that samples within the same family are not mislabelled using their exome sequencing data. I'm sure there must be a tool which takes in vcfs and ped files and can tell you whether the number of Mendelian inconsistences indicate sample mix-up.

Thanks in advance,

Kath

[Bukowski]

GATK SelectVariants allows you to feed it a Plink formatted PED file for e.g. de novo mutations. Abnormally high numbers are a good pointer for a sample mix up.