estimating inbreeding from runs of homozygosity
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?
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Kevin Blighe
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Tears •
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Tears •
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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
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