Question: expected heterozygosity calculation
gravatar for Siavash Salek Ardestani
2.3 years ago by

Hi to all, I have a vcf file that including multisample. I want to calculate expected heterozygosity for this vcf file by sliding-window approach(40-kb-windows slidingin20-kb-steps). I want to know, which software do this? Thanks, Siavash

snp genome vcf • 1.7k views
ADD COMMENTlink written 2.3 years ago by Siavash Salek Ardestani20

Number of hets, hom. ref. and hom. alt. in a given region

bcftools stats -r chr1:23000-26000 -s - <input.vcf.gz>

You are probably interested in runs of homozygosity

bcftools roh
ADD REPLYlink modified 2.3 years ago • written 2.3 years ago by trausch1.5k
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