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

Question

[LDT]

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

Answer 1

[Pierre Lindenbaum]

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

Answer 2

[chrchang523]

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

Answer 3

[hewm2008]

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