Sydney-Informatics-Hub/Fastq-to-BAM

Issues

• not able to run the project

  #26 opened 5 months ago by Shrutiagarwal1805
  1

• bqsr_recal.sh has Empty ref Variable

  #25 opened a year ago by DarioS
  1

• SAMTOOLS_NCPUS is Unused

  #24 opened a year ago by DarioS
  1

• Alternate Contig Alignments and Mapping Quality Zero

  #15 opened 3 years ago by DarioS
  12

• bwa-postalt.js Fail to open the file

  #23 opened a year ago by nandan75
  0

• Reference Bundle is Stored on Deprecated CloudStor Service

  #22 opened a year ago by DarioS
  1

• Reliance on Relative Paths

  #21 opened a year ago by DarioS
  0

• Where to download nci-parallel/1.0.0?

  #20 opened 2 years ago by tkcaccia
  1

• BWA Results Vary Based on Thread Number

  #1 opened 4 years ago by DarioS
  2

• align_make_input.sh lib_diff is Initialised Empty and Never Set Otherwise

  #12 opened 2 years ago by DarioS
  1

• samblaster Path Hard-Coded to Inaccessible Path

  #17 opened 2 years ago by DarioS
  1

• BQSR Recalibration Make Input Only Processes Normal Sample Files

  #18 opened 2 years ago by DarioS
  1

• nci-parallel call needs updating

  #16 opened 3 years ago by calizilla
  0

• Dict Value Assignment Missing

  #13 opened 3 years ago by DarioS
  1

• Question on categories for cohort.config file

  #14 opened 3 years ago by Ysuita
  1

• No fastqc Module on Gadi

  #11 opened 3 years ago by DarioS
  1

• Broken Path to Fixed NCI Parallel

  #7 opened 3 years ago by DarioS
  1

• Split FASTQ Make Input Loses Input Files

  #6 opened 3 years ago by DarioS
  1

• GATK ApplyBQSR Fails if Folder Coincidentally Named unmapped

  #9 opened 3 years ago by DarioS
  1

• reformat_split_disc Removed From Pipeline

  #10 opened 3 years ago by DarioS
  1

• Parallel Align Split FASTQs Has No Checking Script for Failures

  #8 opened 3 years ago by DarioS
  0

• Hard-Coded Dependencies on er01 Scratch

  #2 opened 4 years ago by DarioS
  2