Add samtools mpileup as an alternative variant caller
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enhancement
- Dominant language
- Nextflow
- Stars
- 61
- Forks
- 47
- Avg merge
- 1d 1h
- Merged PRs (30d)
- 1
Description
Description of feature
I tried using the default variants called using GATK but they didn't seem to work as well for my purpose. On the contrary samtools mpileup worked extremely well.
Maybe it would be worthwhile adding it as an alternative calling procedure to this?
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 locating the existing GATK variant-calling procedure in the rnavar pipeline and reviewing how its inputs and outputs are handled. Determine where samtools mpileup could be offered as an alternative, then verify that the pipeline can run with that procedure and produces the expected variant-calling output.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100