Roadmap of BCF(Tools) regarding file size and query performance
Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 20/100
- Issue type
- Feature
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics, performance
Research direction
This issue requests a roadmap for reducing file size and improving query performance in large BCF files, rather than identifying a specific implementation task. It names no files, tests, or entry points to inspect, and completion would require an agreed development direction.
Written by the indexing model from the issue text.
Description
Dear BCF(Tools) developers,
We are happy users of (BCF)Tools for storing and querying whole genome sequencing variant tables of a few hundred to few thousand samples.
File size and query performance are already a bit of an issue with these numbers of samples and certainly will be with 10.000 to 100.000+ samples inside a single BCF file.
I recently followed talks from the the GA4GH workshop with excitement and I am curious about if there already is a roadmap/consensus for including some of these minor or major ideas/features in BCF(Tools)? Or are these development still more in the exploratory phase?
Thank you for the already very nice BCF(Tools) format/software/spec and any information you can share about it's future development.
Edited to be more concise.
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
Contributor guide
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