broadinstitute/GATK-for-Microbes

Issues

• Status?

  #30 opened a year ago by knokknok
  0

• Docker independent pipeline?

  #29 opened 2 years ago by Guan06
  2

• test script fails because ShiftFasta command is missing

  #28 opened 3 years ago by kxw116
  1

• How to build gatk-micobialmode.jar?

  #22 opened 3 years ago by garlandcrow
  4

• Skip revertsam and samtofastq when the input is bam file

  #26 opened 4 years ago by bhanugandham
  0

• Allow users to custom set the memory for the RevertSam task in MicrobialGenomePipeline

  #24 opened 4 years ago by jason-cerrato
  0

• test with recover-all-branches M2 arg

  #21 opened 4 years ago by bhanugandham
  0

• Explain the three output bamouts in documentation

  #14 opened 4 years ago by bhanugandham
  0

• Add an option in the wdl to prefix output files with sample_name

  #12 opened 4 years ago by bhanugandham
  0

• Generate RTG vcfeval summary.txt file as an output concordance wdl

  #10 opened 4 years ago by bhanugandham
  1

• Add joint calling as an option to the pipeline

  #11 opened 4 years ago by bhanugandham
  1

• Make shift fasta optional

  #13 opened 4 years ago by bhanugandham
  0

• Exclude the filtered variants from the filtered.vcf output file

  #16 opened 4 years ago by bhanugandham
  0

• Add a task for Terra UI to hide optional json outputs

  #15 opened 4 years ago by bhanugandham
  0