aryarm / aryarm/as_analysis

extract heterozygotes from the vcf before converting to h5 files

Open
#63 1 comment 0 reactions 0 assignees View on GitHub
enhancement
Dominant language
R
Stars
10
Forks
9
PR merge metrics
No merged PRs in 30d

Description

instead of downstream in the counts subworkflow

Homozygotes aren't useful in allele-specific analyses, so we discard them in the _counts_ subworkflow. But discarding them upstream, even before running WASP, might significantly speed up execution of the pipeline. So are there any downsides to this?

Contributor guide

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Research direction

Begin with the counts subworkflow and the step that converts VCF data to H5 files; inspect where homozygotes are currently discarded and how WASP fits in. Determine whether moving filtering upstream preserves the pipeline’s allele-specific results and quantify any execution benefit before deciding what change is appropriate.

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
30/100

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