tgen/jetstream_resources

Issues

• CHIP updates

  #76 opened 2 years ago by fmadrid2
  0

• Suncity Capture_kits.csv

  #64 opened 2 years ago by PedalheadPHX
  1

• Phoenix Capture Kits

  #65 opened 2 years ago by PedalheadPHX
  1

• T2T GTF

  #69 opened 2 years ago by PedalheadPHX
  0

• Creation of ${GTF_FILE_BASE}.gene.bed and ${GTF_FILE_BASE}.exon.bed needs to operate off column matching

  #58 opened 3 years ago by bryce-turner
  1

• Redundant exons

  #51 opened 3 years ago by PedalheadPHX
  1

• Phoenix - Pairoscope - Region to be skipped - Structural Variant - Exome -TumorOnly

  #49 opened 3 years ago by ChristopheLegendre
  1

• Suncity and non-phoenix HARD PATH VARIABLES

  #19 opened 3 years ago by PedalheadPHX
  1

• Update Salmon for non-phoenix workflows

  #33 opened 3 years ago by PedalheadPHX
  0

• CDS PADDED FILES FOR TMB

  #50 opened 3 years ago by PedalheadPHX
  0

• gnomad VCF includes all variants

  #4 opened 3 years ago by PedalheadPHX
  1

• Phoenix - Add recalculate TPM requirements

  #11 opened 4 years ago by PedalheadPHX
  2

• Update for Copy number centromere and encode and mappability

  #30 opened 4 years ago by PedalheadPHX
  0

• Build/Download DeepVariant Models Fails

  #22 opened 4 years ago by PedalheadPHX
  1

• Need code for building cellRanger files

  #25 opened 4 years ago by PedalheadPHX
  1

• Update README

  #26 opened 4 years ago by PedalheadPHX
  1

• Kappa Locus Correction

  #10 opened 5 years ago by PedalheadPHX
  1

• Delete script from Phoenix

  #15 opened 5 years ago by PedalheadPHX
  0

• Missing exclusion file creation code

  #5 opened 5 years ago by PedalheadPHX
  0

• Need a 1 based regions file for the samtools stats --target-regions FILE

  #7 opened 5 years ago by awchrist
  0

• baits.interval_list is identical to targets.interval_list

  #6 opened 5 years ago by awchrist
  2

• Need to confirm output-type b for annotation reference files

  #9 opened 5 years ago by bryce-turner
  2

• Missing target file for "bcftools stats" command in file "build_gnomAD_r2.1.1.sh"

  #2 opened 5 years ago by ChristopheLegendre
  1

• Add delly annotation code

  #3 opened 5 years ago by PedalheadPHX
  1