concordance metrics for exome trio analysis

Question

[sacha]

I am looking for a metrics to test if mother, father and child from a trio analysis are well assigned to my vcf file. For example the metrics would check if homozygous variants are heterozygous in both parents.

Do you have a metrics or a command line tool for this task ?

Answer 1

[Vivek]

You need to either compute a kinship coefficient or tally the number of mendelian violations. Check KING for doing the analysis. You might need to convert your VCF to PLINK format.