Sample not being detected as edited despite evidence of editing in the bam file
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Description
Description of the bug
I’ve run this pipeline now with a few hundred samples - generally it seems to be working very well. However, I notice that one sample which clearly shows editing in the bam file, is not being detected as edited. Looking at the indels QC file, almost all the reads are not passing filter. However, I can’t see from the bam file why it shouldn’t be passing filter.
Command used and terminal output
No response
Relevant files
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System information
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Contributor guide
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
Start by reproducing the sample in the CRISPRseq pipeline and compare the BAM evidence with the indels QC filtering outcome. The issue names no source file, command, or test, so first locate the step that marks samples as edited and inspect why reads are rejected. Done means the demonstrated edited sample is detected without breaking filtering for other samples.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100