estimating inbreeding from runs of homozygosity

Question

[Tears]

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?

Answer 1

[Kevin Blighe]

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:

• Runs of homozygosity
• Inbreeding

Kevin