CPTR-ReSeqTB/UVP

Issues

• gatk-register command not found

  #35 opened 6 months ago by RuanSpies21
  0

• SnpEff can't find NC_000962.genome

  #20 opened 6 years ago by elenamd
  6

• Exception in analysis

  #34 opened 4 years ago by alantsangmb
  1

• UVP terminates

  #33 opened 4 years ago by AmanuelZewdu
  3

• parse annotation error

  #32 opened 5 years ago by TimHHH
  0

• .fq.gz files not accepted for input

  #30 opened 5 years ago by TimHHH
  0

• invalid literal for int() with base 10: '29.995328591049294\n'

  #31 opened 5 years ago by TimHHH
  0

• Default threads should be 1 not 12

  #14 opened 6 years ago by tseemann
  4

• gatk3/gatk3-register and gatk/gatk-register

  #29 opened 5 years ago by alantsangmb
  2

• Allow users to provide a config file when launching UVP

  #25 opened 5 years ago by dfornika
  3

• Switching to unencumbered GATK 4.x

  #28 opened 5 years ago by tseemann
  5

• file directories

  #27 opened 5 years ago by alantsangmb
  3

• SNPs criteria

  #23 opened 5 years ago by alantsangmb
  2

• Please produce a conda package

  #7 opened 5 years ago by tseemann
  13

• Don't put .txt files in the bin/ folder

  #11 opened 5 years ago by tseemann
  3

• yaml problem

  #22 opened 6 years ago by RichardUABC
  0

• Which kraken database should we use?

  #9 opened 6 years ago by tseemann
  2

• QC directory

  #21 opened 6 years ago by alantsangmb
  2

• Cannot generate GATK_Resilist.grp

  #3 opened 6 years ago by hyunlee11037
  5

• Edit suggested: Escape tab characters to resolve BWA error

  #18 opened 6 years ago by pvishwa2
  1

• "Not species specific" when sample is Mycobacterium Tuberculosis

  #15 opened 6 years ago by matnguyen
  5

• rm: cannot remove ‘Results/test/kraken/kraken.txt’: No such file or directory

  #4 opened 6 years ago by matnguyen
  2

• Include reference genome or risk excluded locii mixup?

  #10 opened 6 years ago by tseemann
  1

• Please use the python in the PATH first

  #5 opened 6 years ago by tseemann
  1

• What LICENSE is this code released under?

  #13 opened 6 years ago by tseemann
  1

• Typo in docs

  #8 opened 6 years ago by tseemann
  1

• Is this python 2 or 3 ?

  #6 opened 6 years ago by tseemann
  3

• fastQValidator subprocess call, OSError: [Errno 2] No such file or directory

  #2 opened 6 years ago by jwcodee
  2