nf-core/sarek

joint genotyping optimal strategy

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#923 opened on Jan 25, 2023

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help wanted

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Description

Working with a large-ish dataset (30TB raw reads), and was wondering what a good strategy would be for working with the joint_germline option to get cohort SNP calls. Would it make more sense to try to genotype all individuals together, or parallelize the joint genotyping runs across smaller groups of samples and then filter and combine with bcftools across jointgermline outputs?

Contributor guide

Research direction
Compare the pros and cons of joint genotyping all samples together versus parallelizing across smaller groups, considering computational resources and accuracy.
Tech stack
None
Domain
backend
Issue type
Research
DifficultyEstimated implementation difficulty for a new contributor, from 1 for very small changes to 5 for expert-level work.
2
Estimated timeA rough time range for an experienced contributor to investigate, implement, test, and prepare a pull request.
1-3 hours
Activity statusHow available the issue appears right now: fresh, active, stale, blocked, or waiting on maintainer input.
Active
ClarityHow clearly the issue explains the expected change, acceptance criteria, and next step.
Clear
Prerequisites
None
Newbie friendlinessA 1-100 score estimating how approachable this issue is for first-time contributors.
70