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concordance metrics for exome trio analysis

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 ?

exome vcf snp

1 answer

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.

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