Summarize insertions
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
Group identical insertions, and report them along with their prevalance as a percentage of coverage at that location.
- Don't report low quality insertions (<Q30).
- Don't report insertions below 1% prevalance.
- Don't report insertions outside of coordinate regions.
- Combine
conseq_ins.csvandcoord_ins.csvinto a single file. - Report insertions from G2P alignment.
- Should we translate insertions into amino acid sequences? We could use the surrounding reading frame, but some insertions are not multiples of three nucleotides or are not inserted at codon boundaries. For now, we have decided to go with the nucleotide sequence.
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
Start by locating the code that produces conseq_ins.csv and coord_ins.csv, then trace how insertion coordinates and coverage are reported. The issue's checklist defines done: combine the outputs, group identical insertions, report prevalence, and apply the stated quality, prevalence, and coordinate filters; G2P alignment remains an open requirement.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100