Expanding dereplicated reads
Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 25/100
- Issue type
- Feature
- Clarity
- Mostly clear
- Activity status
- Stale
- Tech stack
- c
- Domain
- bioinformatics
Research direction
Start by reviewing the mpileup entry point and how its output is consumed by bcftools call. Determine whether dereplication counts can be supplied through a user-defined tag or USEARCH/VSEARCH-style size=X header values without re-expanding reads. Done means depth calculation uses those counts directly and the result remains suitable for bcftools call.
Written by the indexing model from the issue text.
Description
Is your feature request related to a problem? Please specify.
Not really a problem necessarily, but more of a question. Is there currently any way to use information for de-replicated reads when calculating depths via mpileup? The context is that I am working on a serverless pipeline for a de novo assembly of a reduced-representation dataset, with steps running in AWS lambda's, so to keep file sizes and runtimes as small as possible, I'm doing all of the assembly steps using dereplicated reads (with the read counts saved in the headers as ;size=X). Currently I am then re-expanding these to create an intermediate file to send through mpileup before running bcftools call, however I'm wondering if there is a way within samtools to use this count information directly for calculating depths?
Describe the solution you would like.
It would be ideal if samtools could directly parse the count information, for example via a user-defined tag, or by parsing the USEARCH/VSEARCH style size= tags from the headers. If not currently possible, I would be happy to work on it and submit a pull request, but would appreciate some pointers on the best way to proceed.
Thanks!
- Dominant language
- C
- Stars
- 891
- Forks
- 277
- Avg merge
- 2d 23h
- Merged PRs (30d)
- 2
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