Question: expected heterozygosity calculation
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gravatar for siyavash_damdar
17 months ago by
siyavash_damdar20 wrote:

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 • 970 views
ADD COMMENTlink written 17 months ago by siyavash_damdar20

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 17 months ago • written 17 months ago by trausch1.4k
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