Runs of Homozygosity

Question

[Sharon]

When I used BCFtools to calculate ROH, I got all the states for all the positions is zero, a snapshot of the output is below. Does this mean there is no Autozygosity in my sample?

# [1]Chromosome [2]Position     [3]State (0:HW, 1:AZ)   [4]Quality
chr1    13649   0       3.0
chr1    69511   0       99.0
chr1    69552   0       99.0
chr1    664468  0       99.0
chr1    762273  0       99.0
chr1    762589  0       99.0
chr1    865584  0       99.0
chr1    877831  0       99.0
chr1    878325  0       99.0
chr1    881627  0       99.0

[Fabio Marroni]

According to what I understand from the manual (https://samtools.github.io/bcftools/bcftools.html), yes. Is this unexpected?

[Kevin Blighe]

I think that the answer is already in your output. See column header #3:

• HW = Hardy-Weinberg equilibrium (HWE), i.e., the variant satisfies
• HWE AZ = autozygosity

All of your variants have 0, i.e., they satisfy HWE.

The genomic range covered by your variant appears quite large. I'd prefer a greater density of markers for when determining ROH. The determination of ROH is highly variable based on the number of SNPs and the genomic distance that they cover.

Kevin