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Identifying Runs of Homozygosity and Inbreeding Coefficient from VCF File

I had a multi sample vcf file. I now want to identify runs of homozygosity and calculate the wright's inbreeding coefficient for the population. What would be the most straight forward way of doing so? Maybe something like vcftools or any other tool?

snp vcf genomics
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updated by Ram Ram • written by saamhasan55 • saamhasan55

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written by Pierre Lindenbaum Pierre Lindenbaum

2 answers

Try Plink tools. you can find it here

https://www.cog-genomics.org/plink/2.0/

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written by SomeOne • SomeOne

you should add how to use plink to identify "Runs of Homozygosity and Inbreeding Coefficient from VCF File"

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written by Pierre Lindenbaum Pierre Lindenbaum

to detect ROH , there is bcftools: https://samtools.github.io/bcftools/howtos/roh-calling.html

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written by Pierre Lindenbaum Pierre Lindenbaum

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