Question

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

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2.1 years ago

LDT ▴ 340

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 • 2.1k views

ADD COMMENT • link updated 6 months ago by hewm2008 ▴ 50 • written 2.1 years ago by LDT ▴ 340

score 2 · Answer 1 · 2022-11-08

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2.1 years ago

Pierre Lindenbaum 164k

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

ADD COMMENT • link 2.1 years ago by Pierre Lindenbaum 164k

score 1 · Answer 2 · 2022-11-08

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2.1 years ago

chrchang523 11k

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

ADD COMMENT • link 2.1 years ago by chrchang523 11k

score 1 · Answer 3 · 2024-06-16

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6 months ago

hewm2008 ▴ 50

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

ADD COMMENT • link 6 months ago by hewm2008 ▴ 50