nf-core/rnavar

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gatk4 RNA variant calling pipeline

Stars: 61
Forks: 47
Open beginner issues: 0
Indexed issues: 22
Avg merge: 1d 1h
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

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22 open issues indexed

RNAVAR:GATK4_VARIANTFILTRATION fails when using integer thresholds (NumberFormatException) Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 65/100

nf-core/rnavar#304 · Opened May 15, 2026
BUG NFCORE_RNAVAR:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/rnavar#299 · Opened Apr 23, 2026
rnavar workflow metro map suggestion Open

enhancement

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

nf-core/rnavar#298 · Opened Apr 14, 2026
Support for merged output Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 30/100

nf-core/rnavar#271 · 1 comment · Opened Dec 17, 2025
Integrating VCF2MAF ? Open

enhancement

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

nf-core/rnavar#258 · Opened Nov 5, 2025
Tumour-only somatic variant calling Open

enhancement

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

nf-core/rnavar#241 · 1 reaction · Opened Sep 30, 2025
FILTER column empty and no annotation output Open

bug

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

nf-core/rnavar#236 · Opened Sep 7, 2025
Check if all files in nft-ignore are actually unstable or even produced Open

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

nf-core/rnavar#226 · Opened Aug 25, 2025
samtools not indexing in csi Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 45/100

nf-core/rnavar#217 · 2 comments · Opened Jul 11, 2025
GATK4_MERGEVCFS not sorted Open

bug

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

nf-core/rnavar#214 · 2 comments · Opened Jul 7, 2025
Adding a field for custom params for STAR Open

enhancement

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

nf-core/rnavar#207 · Opened May 3, 2025
Add minimap2 Open

enhancement

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

nf-core/rnavar#205 · 1 reaction · Opened Apr 20, 2025
Adding support for somatic variant calling (MuTect2) Open

enhancement

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

nf-core/rnavar#204 · Opened Apr 10, 2025
Variant annotation VEP plugins Open

enhancement

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

nf-core/rnavar#189 · Opened Mar 6, 2025
Add samtools markdup for UMI aware markdup Open

enhancement

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

nf-core/rnavar#181 · Opened Mar 3, 2025
Thoughts on submitting RNAVar to a journal? Open

question

Difficulty 5/5 Over a week Newbie friendliness 15/100

nf-core/rnavar#147 · 3 reactions · Opened Jun 26, 2024
Add samtools mpileup as an alternative variant caller Open

enhancement

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

nf-core/rnavar#110 · 1 reaction · Opened Nov 28, 2023
Add `trimming` step Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 28/100

nf-core/rnavar#96 · Opened Aug 15, 2023
Single cell somatic mutations Open

enhancement

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

nf-core/rnavar#77 · 1 comment · Opened Nov 22, 2022
Optional filter out RNA editing variants Open

enhancement

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

nf-core/rnavar#63 · 1 reaction · Opened Jun 29, 2022
Summary metrics of haplotypecaller.filtered.vcf Open

enhancement

nf-core/rnavar#59 · 1 comment · 1 assignee · Opened Jun 20, 2022
SIFT missense predictions for genomes Open

enhancement

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

nf-core/rnavar#20 · Opened Feb 1, 2022

nf-core/rnavar

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