Issues

• Pipeline level snapshots

  enhancementlow priority
  nf-core/variantbenchmarking#350 · Filter by author kubranarci opened on Oct 16, 2026

• hap.py benchmarking silently produces empty results for GRCh37/b37 (non-chr-prefixed) references

  nf-core/variantbenchmarking#324 · Filter by author mbiob opened on Sep 15, 2026
  1

• some of test configs under conf/ are outdated

  bug
  nf-core/variantbenchmarking#321 · Filter by author kubranarci opened on Aug 26, 2026
  2

• Running analysis on sample sample id's

  nf-core/variantbenchmarking#307 · Filter by author Indianhedgehog opened on May 19, 2026
  3

• Label change for process VCF_TO_CSV

  enhancement
  nf-core/variantbenchmarking#306 · Filter by author Stautis opened on May 15, 2026
  5

• vcf_variant_filtering

  low priority
  nf-core/variantbenchmarking#293 · Filter by author georgiakes opened on Mar 13, 2026
  

• wittyer_benchmark

  low priority
  nf-core/variantbenchmarking#291 · Filter by author BarrecaM opened on Mar 12, 2026
  

• svanalyser_benchmark

  low priority
  nf-core/variantbenchmarking#285 · Filter by author sceriff0 opened on Mar 11, 2026
  

• happy_benchmark

  low priority
  nf-core/variantbenchmarking#284 · Filter by author erbatto opened on Mar 11, 2026
  

• vcf_to_csv -> gatk4/variantstotable

  enhancementlow priority
  nf-core/variantbenchmarking#280 · Filter by author kubranarci opened on Mar 10, 2026
  

• Port local subworkflows to nf-core/modules

  enhancementgood first issuelow priority
  nf-core/variantbenchmarking#265 · Filter by author georgiakes opened on Jan 22, 2026
  2

• Port local modules to nf-core/modules

  enhancementlow priority
  nf-core/variantbenchmarking#264 · Filter by author georgiakes opened on Jan 22, 2026
  5

• add TP_comp for sompy

  bugenhancement
  nf-core/variantbenchmarking#233 · Filter by author kubranarci opened on Oct 14, 2025

• unexpected F1 score running somatic snv/indel variants benchmarking

  bug
  nf-core/variantbenchmarking#225 · Filter by author gianfilippo opened on Sep 29, 2025
  10

• Multiple truth sets within the same run

  enhancementnot urgent
  nf-core/variantbenchmarking#202 · Filter by author fellen31 opened on Jun 5, 2025
  3

• add vcfdist tool for benchmarking

  enhancementgood first issue
  nf-core/variantbenchmarking#199 · Filter by author kubranarci opened on Jun 3, 2025
  

• SEQC2 test fails for rtgtools as malformatted INFO field in the truth

  bug
  nf-core/variantbenchmarking#186 · Filter by author kubranarci opened on Apr 17, 2025
  1

• igv-reports

  backlogenhancementlow priority
  nf-core/variantbenchmarking#184 · Filter by author kubranarci opened on Apr 16, 2025

• add total stats for happy merging snps and indels

  backlogenhancement
  nf-core/variantbenchmarking#183 · Filter by author kubranarci opened on Apr 16, 2025

• improve plots/statistics

  nf-core/variantbenchmarking#180 · Filter by author kubranarci opened on Apr 7, 2025

• vt decompose_blocksub

  enhancementgood first issue
  nf-core/variantbenchmarking#114 · Filter by author kubranarci opened on Dec 2, 2024

• somatic workflow

  nf-core/variantbenchmarking#96 · Filter by author kubranarci opened on Oct 22, 2024

• generate somatic test files for COLO-829

  backlogenhancementnot urgent
  Task

  nf-core/variantbenchmarking#93 · Filter by author kubranarci opened on Oct 22, 2024

• oncoliner assessment tool

  enhancementnot urgent
  nf-core/variantbenchmarking#92 · Filter by author kubranarci opened on Oct 14, 2024

• add oncoliner tools

  enhancementnot urgent
  nf-core/variantbenchmarking#89 · Filter by author kubranarci opened on Sep 25, 2024