Question: estimating inbreeding from runs of homozygosity
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gravatar for Tears
15 months ago by
Tears 0
Tears 0 wrote:

Hello,

I am using data genotyped on 777K and 150K to estimate the level of relatedness in cattle.

the formula is as follows F=L_roh/L_auto, where L_roh is the sum of ROH per individual and L_auto is the total length of the autosome covered by snps.

How do I estimate the length of the autosomal genome covered by SNPs?

snp roh • 815 views
ADD COMMENTlink modified 15 months ago by Kevin Blighe42k • written 15 months ago by Tears 0
0
gravatar for Kevin Blighe
15 months ago by
Kevin Blighe42k
Republic of Ireland
Kevin Blighe42k wrote:

If your data is in VCF or BCF format (most likely not considering you have microarray data), then you can use BCFtools to calculate both ROH and the inbreeding coefficient: BCFtools/RoH: a hidden Markov model approach for detecting autozygosity from next-generation sequencing data.

If your data is in PLINK format, then you can also do it there:

Kevin

ADD COMMENTlink modified 15 months ago • written 15 months ago by Kevin Blighe42k
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