How to filter the results of roh

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Assessment

Difficulty
3/5
Estimated time
1-2 days
Newbie friendliness
25/100
Issue type
Documentation
Clarity
Needs clarification
Activity status
Stale
Domain
cli, documentation

Research direction

Start with the bcftools roh -G30 -e - -O r vcf.gz command and the roh output documentation. Determine what Quality (average fwd-bwd phred score) represents and whether it can support filtering high-quality regions; done means documenting the interpretation and any appropriate filtering guidance.

Written by the indexing model from the issue text.

Description

Dear @pd3

I am using bcftools roh (version 1.12; bcftools roh -G30 -e - -O r vcf.gz) to detect regions of autozygosity in whole genome sequencing data. The vcf.gz contains all my studied samples which can be clustered into five different populations, and I want to characterize the autozygosity for each population. After running above command, it reports the candidate RoHs for each sample. I can understand most of the output, however, I cannot find some detailed explaination about the Quality (average fwd-bwd phred score)? If I want to filter for high quality regions of autozygosity, can Quality be used as an indicator? The larger of Quality, the higher quality of the RoHs, is this right?

Best regards,
Zheng zhuqing

Dominant language
C
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Forks
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Avg merge
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Merged PRs (30d)
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