nf-core/raredisease

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Call and score variants from WGS/WES of rare disease patients.

Stars: 124
Forks: 70
Open beginner issues: 0
Indexed issues: 21
Avg merge: 1d 23h
Merged PRs (30d): 38

Dominant language: Nextflow
License: MIT
Last GitHub push: Jul 28, 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

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21 open issues indexed

Convert UPD bed files to bigBed format Open

enhancement

Difficulty 2/5 1-3 hours Newbie friendliness 74/100

nf-core/raredisease#1029 · Opened Sep 16, 2026
Pipeline not using fasta from igenomes Open

bug

Difficulty 2/5 1-3 hours Newbie friendliness 68/100

nf-core/raredisease#934 · 1 comment · Opened Jul 17, 2026
Unsafe pattern in `annotate_genome_snvs`? Open

bug

nf-core/raredisease#868 · 2 assignees · Opened Jun 1, 2026
Add optional parameters for SV/SNV filtering and calling configuration Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 48/100

nf-core/raredisease#822 · Opened Apr 27, 2026
cnvnator/cnvnator: Wave container fails with missing assert.h on Red Hat Enterprise Linux 8 Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/raredisease#817 · 3 comments · Opened Apr 20, 2026
Add MIVMIR, GICAM models for SNV ranking Open

enhancement

nf-core/raredisease#816 · 2 assignees · Opened Apr 20, 2026
SPLIT_MULTIALLELICS_SEN: --multiallelics -both causes indel precision degradation (~4%) in single-interval runs Open

bug

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

nf-core/raredisease#813 · 15 comments · Opened Apr 16, 2026
Restrict variant calling and annotations to certain regions Open

enhancement

nf-core/raredisease#740 · 1 comment · 1 assignee · Opened Nov 14, 2025
test config igenome configurations are wrong Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/raredisease#681 · 1 comment · Opened Feb 25, 2025
To fix before next releases Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/raredisease#663 · 3 comments · 1 reaction · Opened Jan 15, 2025
Mosdepth coverage report of WES regions Open

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

nf-core/raredisease#645 · Opened Nov 10, 2024
gnomAD v4.1 SV database contains mix of SV and CNV - svdb problem Open

bug

nf-core/raredisease#615 · 1 comment · 2 reactions · 1 assignee · Opened Sep 20, 2024
Split deepvariant pipeline Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

nf-core/raredisease#614 · 1 comment · 2 reactions · Opened Sep 20, 2024
Allow multiple unrelated cases/families in samplesheet.csv Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/raredisease#604 · 1 comment · Opened Aug 22, 2024
https://ai.marrvel.org / how to integrate to Scout and our analysis? Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

nf-core/raredisease#560 · 5 comments · Opened May 27, 2024
use estimated sex in analysis Open

enhancement

nf-core/raredisease#465 · 1 assignee · Opened Jan 8, 2024
DeepMind AlphaMissense Open

Effort low enhancement on hold

Difficulty 4/5 3-5 days Newbie friendliness 45/100

nf-core/raredisease#427 · 9 comments · 2 reactions · Opened Sep 20, 2023
Add BPHunter Open

feature-request on hold

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

nf-core/raredisease#424 · Opened Sep 11, 2023
Customize aws full pipeline tests Open

enhancement

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

nf-core/raredisease#318 · Opened Mar 25, 2023
Add full sized test dataset Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

nf-core/raredisease#316 · Opened Mar 25, 2023
WisecondorX for aneuploidy and gender detection Open

enhancement

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

nf-core/raredisease#198 · 1 comment · 1 reaction · Opened Aug 3, 2022

nf-core/raredisease

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