Identifying Runs of Homozygosity and Inbreeding Coefficient from VCF File
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18 days ago
saamhasan55 ▴ 10

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 • 399 views
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18 days ago
Umer ▴ 130

Try Plink tools. you can find it here

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

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

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18 days ago

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

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