bcftools roh number of markers
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Assessment
- Difficulty
- 2/5
- Estimated time
- 1-3 hours
- Newbie friendliness
- 30/100
- Issue type
- Documentation
- Clarity
- Needs clarification
- Activity status
- Stale
- Domain
- documentation
Research direction
Review the bcftools roh documentation alongside the reported output table. Clarify what “number of markers” and “length (bp)” mean, how ROH lengths should be aggregated, and why the example values differ; done when these questions are answered directly in the documentation.
Written by the indexing model from the issue text.
Description
Hello
I am unable to find the definition of markers in the bcftools roh documentation.
Can you please explain what is the meaning of number of markers here and why does it not match the ROH length of 12747 in this example?
Is the total length of ROH for this region to be estimated as length multiplied by the number of makers ? if not how does one know what is the average length of ROHs for our sample, and what is the total length of all ROHs across the genome?
Is the length really in bp, as the largest length in my database is 30 kb.
RG [2]Sample [3]Chromosome [4]Start [5]End [6]Length (bp) [7]Number of markers [8]Quality
RG sample.bam Chromosome25 100 12846 12747 23 32.2
Thank you for your help,
Shaili.
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