nf-core/phaseimpute

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A bioinformatics pipeline to phase and impute genetic data

Stars: 35
Forks: 23
Open beginner issues: 0
Indexed issues: 14
Avg merge: 16d 3h
Merged PRs (30d): 1

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 27, 2026
Latest indexed: Sep 19, 2026
Contributing guide: Contributing guide
Code of conduct: Code of conduct
Beginner labels: No beginner labels indexed

Beginner friendly Everything

Open All

14 open issues indexed

Minimac4 with unphased data Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 38/100

nf-core/phaseimpute#311 · Opened Sep 15, 2026
Csv samplesheet with only one individual Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

nf-core/phaseimpute#310 · Opened Sep 15, 2026
Genetic map samplesheet validation rejects non-standard chromosome names Open

enhancement

nf-core/phaseimpute#306 · 2 comments · 1 assignee · Opened Aug 21, 2026
Add support for single file genetic compressed file Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 38/100

nf-core/phaseimpute#305 · Opened Aug 11, 2026
Add fasta existence check for prepare_genome Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 55/100

nf-core/phaseimpute#304 · Opened Aug 11, 2026
Improve performance and resource usage in imputation tools Open

enhancement

nf-core/phaseimpute#295 · 1 assignee · Opened May 24, 2026
Add post-imputation filter step Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 48/100

nf-core/phaseimpute#287 · Opened Apr 30, 2026
Check channel join Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 30/100

nf-core/phaseimpute#241 · Opened Dec 16, 2025
Use sites VCF to select variants to impute and clarify posfile.csv Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/phaseimpute#212 · Opened Nov 13, 2025
Add phase_rare to phasing subworkflow Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 42/100

nf-core/phaseimpute#207 · Opened Sep 24, 2025
Use of multiple panel at once Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 42/100

nf-core/phaseimpute#191 · Opened Apr 29, 2025
Contribute back to nf-core Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/phaseimpute#112 · 2 comments · Opened Jul 22, 2024
Panel chunking Open

enhancement

nf-core/phaseimpute#95 · 3 comments · 1 assignee · Opened Jul 3, 2024
Imputation of chrX Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

nf-core/phaseimpute#31 · Opened Apr 22, 2024

nf-core/phaseimpute

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