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How to measure pairwise genetic distance in all samples of a VCF file

Dear all,

I have a large VCF file with more than 1000 samples, aka genomes. I want to find which samples are closely related and which are not by measuring the pairwise genetic distance of these files.

Which is your favourite software to calculate this metric?

Thank you for your time

pop-gen pairwise-distance vcf
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updated by hewm2008 • hewm2008 • written by LDT • LDT

3 answers

try somalier https://github.com/brentp/somalier

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written by Pierre Lindenbaum Pierre Lindenbaum

"plink2 --vcf ... --make-king-table"

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written by chrchang523 chrchang523

you can try this tools :https://github.com/BGI-shenzhen/VCF2Dis

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written by hewm2008 • hewm2008

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