Interpreting output of BCFtools RoH
I am using BCFtools RoH for the first time, and I am having some trouble understanding its output file.
The input is a gvcf file with genotype calls for one sample only, and I want to infer where there might be autozygous tracts. The command line I used is this one: bcftools roh -G30 –AF-dflt 0.4 –output output_name my.input.vcf.gz
Now, in the output there are state lines (ST) and region lines (RG). How should these be interpreted? I understand that state lines refer to 1 site at a time only, while region lines flag that all sites in the given interval are autozygous. When visualizing this output, are thus the region lines the only ones that can be considered RoH?
These region lines appear sparsely along the file but seemingly not following a strict numerical order with the state lines. Here goes an example of a region line, the line immediately before and the one immediately after:
ST sample chrom 3106762 0 49.6
RG sample chrom 2923930 3106746 182817 118 42.7
ST sample chrom 3106790 0 39.3
Any hints on how to interpret and visualize the output of BCFtools RoH?
Thanks in advance!
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