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How to do an plink IBD analysis using vcfs from WES

I have about 300 single-sample VCFs from WES，I want to do an IBD analysis to calculate the pihat value so that I can confirm the 300 individuals are not related.

But,emmm... I'm totally new to plink. I have read the manual but still can't figure out how to use singe-sample vcf to do that.

Can someone tell me the procedure?or an example?

Thanks in advance for any help!

snp sequencing
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updated by Kevin Blighe Kevin Blighe • written by dioncst • dioncst

1 answer

Here is a working tutorial for 1000 Genomes Phase III VCFs: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format

At step 10, after you have your data in PLINK format, just run the standard commands for generating IBD matrices with PLINK.

Kevin

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written by Kevin Blighe Kevin Blighe

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