Question: concordance metrics for exome trio analysis
0
gravatar for sacha
3 months ago by
sacha1.9k
France
sacha1.9k wrote:

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 ?

snp vcf exome • 142 views
ADD COMMENTlink modified 3 months ago by Vivek2.4k • written 3 months ago by sacha1.9k
2
gravatar for Vivek
3 months ago by
Vivek2.4k
Denmark
Vivek2.4k wrote:

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.

ADD COMMENTlink modified 3 months ago • written 3 months ago by Vivek2.4k
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