Identifying Runs of Homozygosity and Inbreeding Coefficient from VCF File

Question

[saamhasan55]

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?

[Pierre Lindenbaum]

Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

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Answer 1

[Umer]

Try Plink tools. you can find it here

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

[Pierre Lindenbaum]

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

Answer 2

[Pierre Lindenbaum]

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