Issues

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

  bug
  nf-core/rnavar#304 · Filter by author pablolopeznie opened on May 15, 2026

• BUG NFCORE_RNAVAR:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY

  bug
  nf-core/rnavar#299 · Filter by author robinjugas opened on Apr 23, 2026

• rnavar workflow metro map suggestion

  enhancement
  nf-core/rnavar#298 · Filter by author pablolopeznie opened on Apr 14, 2026

• Support for merged output

  enhancement
  nf-core/rnavar#271 · Filter by author mylena-s opened on Dec 17, 2025
  1

• Integrating VCF2MAF ?

  enhancement
  nf-core/rnavar#258 · Filter by author ZWael opened on Nov 5, 2025

• Tumour-only somatic variant calling

  enhancement
  nf-core/rnavar#241 · Filter by author chstubbe opened on Sep 30, 2025

• FILTER column empty and no annotation output

  bug
  nf-core/rnavar#236 · Filter by author gianfilippo opened on Sep 7, 2025

• Check if all files in nft-ignore are actually unstable or even produced

  nf-core/rnavar#226 · Filter by author maxulysse opened on Aug 25, 2025

• samtools not indexing in csi

  bug
  nf-core/rnavar#217 · Filter by author altuffin opened on Jul 11, 2025
  2

• GATK4_MERGEVCFS not sorted

  bug
  nf-core/rnavar#214 · Filter by author yannic-chen opened on Jul 7, 2025
  2

• Adding a field for custom params for STAR

  enhancement
  nf-core/rnavar#207 · Filter by author genomaxx opened on May 3, 2025

• Add minimap2

  enhancement
  nf-core/rnavar#205 · Filter by author maxulysse opened on Apr 20, 2025

• Adding support for somatic variant calling (MuTect2)

  enhancement
  nf-core/rnavar#204 · Filter by author amizeranschi opened on Apr 10, 2025

• Variant annotation VEP plugins

  enhancement
  nf-core/rnavar#189 · Filter by author ntmytran opened on Mar 6, 2025 · 1.2.0

• Add samtools markdup for UMI aware markdup

  enhancement
  nf-core/rnavar#181 · Filter by author matthdsm opened on Mar 3, 2025 · 1.2.0

• Thoughts on submitting RNAVar to a journal?

  question
  nf-core/rnavar#147 · Filter by author Shaun-Regenbaum opened on Jun 26, 2024 · 1.2.0

• Add samtools mpileup as an alternative variant caller

  enhancement
  nf-core/rnavar#110 · Filter by author Leon-Bichmann opened on Nov 28, 2023 · 1.2.0

• Add trimming step

  enhancement
  nf-core/rnavar#96 · Filter by author bounlu opened on Aug 15, 2023 · 1.2.0

• Single cell somatic mutations

  enhancement
  nf-core/rnavar#77 · Filter by author cutleraging opened on Nov 22, 2022 · 1.2.0
  1

• Optional filter out RNA editing variants

  enhancement
  nf-core/rnavar#63 · Filter by author ojziff opened on Jun 29, 2022 · 1.2.0

• Summary metrics of haplotypecaller.filtered.vcf

  enhancement
  nf-core/rnavar#59 · Filter by author ojziff opened on Jun 20, 2022 · 1.2.0
  1

  

• SIFT missense predictions for genomes

  enhancement
  nf-core/rnavar#20 · Filter by author m3hdad opened on Feb 1, 2022 · 1.2.0