Issues

• Non-blocking issues with standalone pipelines

  bug
  NBISweden/biovat#136 · Filter by author CormacKinsella opened on Nov 2, 2026
  

• Check that BAM/CRAM input matches the reference

  NBISweden/biovat#135 · Filter by author mahesh-panchal opened on Oct 30, 2026

• vcftools --TsTv-by-count crashes on some small callsets and fails the run

  bug
  NBISweden/biovat#134 · Filter by author mahesh-panchal opened on Oct 28, 2026

• Filter outputs at publish, not within the workflow

  enhancement
  NBISweden/biovat#133 · Filter by author CormacKinsella opened on Oct 28, 2026
  1

  

• Support long reads

  enhancement
  NBISweden/biovat#130 · Filter by author CormacKinsella opened on Oct 16, 2026 · TDP 3: additional data types

• GATK open issues

  NBISweden/biovat#128 · Filter by author CormacKinsella opened on Oct 12, 2026 · 2: data processing and filtering of mapped whole genome re-sequencing data
  1

• Add an AI-disclosure convention to CONTRIBUTING

  NBISweden/biovat#126 · Filter by author mahesh-panchal opened on Oct 9, 2026
  2

• Multi-platform variant calling

  question
  NBISweden/biovat#125 · Filter by author CormacKinsella opened on Oct 8, 2026 · TDP 3: additional data types

• Params to consider exposing to users

  enhancementquestion
  NBISweden/biovat#124 · Filter by author CormacKinsella opened on Oct 8, 2026 · 2: data processing and filtering of mapped whole genome re-sequencing data

• vcftools filter.summary bug

  bug
  NBISweden/biovat#123 · Filter by author CormacKinsella opened on Oct 7, 2026 · 2: data processing and filtering of mapped whole genome re-sequencing data
  

• Feature: Implement Parabricks versions of GATK haplotypeCaller and genotypeGVCFs

  enhancement
  NBISweden/biovat#114 · Filter by author verku opened on Sep 30, 2026 · 2: data processing and filtering of mapped whole genome re-sequencing data
  

• Extend test coverage

  enhancement
  NBISweden/biovat#108 · Filter by author CormacKinsella opened on Sep 21, 2026 · TDP 4: pipeline launch (end delivery)
  2

• Create a repository to try out BioVAT with a small test dataset

  documentationenhancement
  NBISweden/biovat#105 · Filter by author verku opened on Sep 18, 2026 · TDP 4: pipeline launch (end delivery)
  

• Feature: Implement bcftools mpileup/call for multi-sample and per-sample variant calling

  enhancement
  NBISweden/biovat#104 · Filter by author verku opened on Sep 18, 2026 · 2: data processing and filtering of mapped whole genome re-sequencing data
  5

  

• Provide a small dataset for pipeline testing to produce biologically meaningful results

  enhancement
  NBISweden/biovat#102 · Filter by author verku opened on Sep 17, 2026 · 3: variant filtering for whole genome re-sequencing data
  

• Add reference sequence header sanitizing step

  enhancementfeedback needed
  NBISweden/biovat#101 · Filter by author mahesh-panchal opened on Sep 17, 2026 · TDP 2: core pipeline finalized
  1

• GPU deduplication

  enhancement
  NBISweden/biovat#100 · Filter by author CormacKinsella opened on Sep 17, 2026 · 1: data processing and filtering of raw whole genome re-sequencing data
  

• Pipeline stages: raw reads to raw variant calls (short-read whole genome re-sequencing data)

  ADR
  NBISweden/biovat#95 · Filter by author verku opened on Sep 11, 2026 · TDP 1: structure and content planning
  2

  

• Outputs: enable_output_intermediates

  enhancementfeedback needed
  NBISweden/biovat#94 · Filter by author CormacKinsella opened on Sep 11, 2026 · TDP 1: structure and content planning
  3

  

• Platform to file prefix or destination path?

  NBISweden/biovat#91 · Filter by author CormacKinsella opened on Sep 11, 2026 · TDP 1: structure and content planning
  2

• Pending MultiQC v1.36: Remove temporary fix

  NBISweden/biovat#89 · Filter by author CormacKinsella opened on Sep 10, 2026

• Implement subworkflow for reference quality checks

  enhancementfeedback neededgood first issue
  NBISweden/biovat#86 · Filter by author verku opened on Sep 3, 2026 · TDP 2: core pipeline finalized
  9

  

• Bug: remote files downloaded to cache directory under work/

  bug
  NBISweden/biovat#83 · Filter by author verku opened on Sep 3, 2026 · 1: data processing and filtering of raw whole genome re-sequencing data

• Implement clam stat to calculate population genetic statistics from a VCF using callable site information

  enhancement
  NBISweden/biovat#80 · Filter by author verku opened on Sep 2, 2026 · 4: population genomics downstream analyses for whole genome re-sequencing data

• Implement clam subworkflow

  enhancement
  NBISweden/biovat#79 · Filter by author verku opened on Sep 2, 2026 · 4: population genomics downstream analyses for whole genome re-sequencing data