concordance metrics for exome trio analysis
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4.4 years ago
sacha ★ 2.4k

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 • 979 views
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Entering edit mode
4.4 years ago
Vivek ★ 2.7k

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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