Runs of Homozygosity
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
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According to what I understand from the manual (https://samtools.github.io/bcftools/bcftools.html), yes. Is this unexpected?
I think that the answer is already in your output. See column header #3:
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