icgc-argo-workflows/gatk-mutect2-variant-calling

Issues

• Update the `song_score_upload` and `song_score_download` modules to latest versions

  #33 opened a year ago by lindaxiang
  1

• Investigating failed Mutect2 calling on DO50311

  #31 opened 4 years ago by junjun-zhang
  0

• update payload gen variant calling package to 0.5.0

  #29 opened 4 years ago by junjun-zhang
  1

• Update workflow to use updated payload gen tool package

  #27 opened 4 years ago by junjun-zhang
  1

• Update to latest version of dependent modules

  #19 opened 4 years ago by junjun-zhang
  1

• Refine input params for mutect2 workflow

  #8 opened 4 years ago by junjun-zhang
  2

• tools needed for payload generation for mutect2 snv_mnv and indel calls, and QC metrics

  #11 opened 4 years ago by junjun-zhang
  1

• Update calculate contamination subworkflow to include normal sample

  #14 opened 4 years ago by junjun-zhang
  1

• upgrade the song/score modules to 2.1.0

  #13 opened 4 years ago by junjun-zhang
  1

• add a param to control whether or not to run BQSR

  #10 opened 4 years ago by junjun-zhang
  1

• Add a step to split original raw mutect2 VCF into two VCFs each contain SNV/MNV and InDel calls

  #9 opened 4 years ago by junjun-zhang
  1

• Potential file name conflict at calCont step in calculateContamination subworkflow

  #7 opened 4 years ago by junjun-zhang
  1

• Drop alignment artifact filtering step which is marked as experimental tool in GATK

  #6 opened 4 years ago by junjun-zhang
  1

• starting from af-only-gnomad.hg38.vcf.gz prepare PASS only, biallelic only resouce file for mutect2 workflow

  #5 opened 4 years ago by junjun-zhang
  2

• Duplicated identical reads in BAM produced by GatherBamFiles tool

  #3 opened 4 years ago by junjun-zhang
  2

• Complete calculate-contamination NF sub-workflow

  #2 opened 4 years ago by junjun-zhang
  1

• Complete BQSR subworkflow

  #1 opened 4 years ago by junjun-zhang
  1