Throw warning when genotyping with pileupcaller on single-stranded libraries that were PE and not collapsed
Nobody has claimed this yet.
- Dominant language
- Nextflow
- Stars
- 215
- Forks
- 91
- Avg merge
- 5m
- Merged PRs (30d)
- 1
Description
See https://github.com/stschiff/sequenceTools/issues/24
In cases where PE un-collapsed reads from a single-stranded library are used in pileupcaller, the damage model is off, and damage artefacts will still make it into the genotypes.
Maybe we should throw a warning when a user specifies pileupcaller as the genotyper while also opting to --skip_collapse?
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
Inspect the pileupcaller configuration and the handling of --skip_collapse to find where incompatible options are validated. Confirm the warning condition for paired-end, uncollapsed reads from single-stranded libraries, and verify that users are warned when pileupcaller is selected with --skip_collapse.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100