what do the bcftools ROH output "markers & quality" fields indicate ?

Question

[Inquisitive8995]

Hello all,

I understand this is a very basic question but I am unable to find the explanation for the 2 columns in bcftools ROH output. I went through their manual in https://samtools.github.io/bcftools/howtos/roh-calling.html. But could not find the output format explanation.

The header looks like this

# RG    [2]Sample       [3]Chromosome   [4]Start        [5]End  [6]Length (bp)  [7]Number of markers    [8]Quality (average fwd-bwd phred score)

What is RG, Number of Markers and Quality indicate.

I presumed the Number of markers are the SNPs present but the below line in my output shows more markers than the length of homozygous region.

RG      sample1     1  66881536        66889308        7773    46939   84.5

I have several positions like this. Any help would be appreciated.

Answer 1

[XiBon]

I have the same question. What is RG and are the regions contained in the *bcf.txt.gz file the homozygous regions? I cannot find documentation on bcftoolsRoH's output

[Inquisitive8995]

I am not sure if this is the correct answer but I think I figured out what RG and ST can be. When you use multiple sample VCF file, it calculates ROH over a region (RG) but when you use a single sample VCF file, it gives you the state (ST; either HW or AZ)

[taniamahmood38]

Thank you so much for making it clear. But I have a question that ROH is an intrapopulation approach. Then what is the logic to use multiple sample VCF file for the analysis? Kindly elaborate on that.

Thank you in advance