Use BAQ when merging reads?
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- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
The samtools mpileup command uses per-base alignment quality (BAQ) to recalculate the quality score of bases that have been merged from the forward and reverse reads. This is described in the manual as:
probabilistic realignment for the computation of base alignment quality (BAQ). BAQ is the Phred-scaled probability of a read base being misaligned. Applying this option greatly helps to reduce false SNPs caused by misalignments.
There is some discussion of whether to disable this with the -B option or to use a different calculation with the -E option.
Currently, we just use the highest quality of the two bases when merging a forward and reverse read pair. Should we use some form of the BAQ calculation?
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No implementation file or test is named in the issue. Start by locating the code that merges forward and reverse bases, then compare its current highest-quality behavior with samtools mpileup BAQ and the documented -B and -E alternatives. Done means a decided BAQ-compatible behavior backed by tests.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100