nf-core / nf-core/variantprioritization
Handling of multiple germline VCFs per sample
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enhancement
- Dominant language
- Nextflow
- Stars
- 16
- Forks
- 11
- PR merge metrics
- No merged PRs in 30d
Description
Description of feature
We could add a sensible default for handling mutliple germline VCFs per sample (for example when multiple callers have been applied to the same sample as done in nf-core/sarek).
This could be some simple concatenation or a consensus approach. Also see https://github.com/sigven/cpsr/issues/72.
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 reviewing how nf-core/sarek handles multiple germline VCFs per sample and the related discussion in cpsr#72. Clarify whether concatenation or consensus is required, then define the supported default behavior and verify that the pipeline handles multiple VCFs consistently.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100