TrinityCTAT/ctat-mutations

Issues

• Not able to run CTAT Mutations

  #135 opened 6 months ago by mariasolruiz
  38

• mutation-lib supplement for GRCm39

  #134 opened 7 months ago by cachedpotato
  10

• hg19 igv report html appears broken (works fine for hg38 though)

  #132 opened 7 months ago by brianjohnhaas
  0

• dbSNP frequence question

  #131 opened 9 months ago by teresa1997
  1

• Missing path to CTAT_GENOME_LIB

  #130 opened a year ago by teresa1997
  5

• Issue with BQSR maximum cycle value

  #129 opened a year ago by irzamsarfraz
  1

• k8 missing from Container

  #128 opened a year ago by readline
  5

• Annotate CRAVAT error

  #126 opened a year ago by gianfilippo
  18

• allow for igv-reports if filtering set to none

  #127 opened a year ago by brianjohnhaas
  0

• pipeline extremely slow: stuck at "Annotate PASS Reads"

  #112 opened 2 years ago by gianfilippo
  40

• zipfile.BadZipFile: File is not a zip file

  #124 opened 2 years ago by wx904
  3

• Annotating VCF at BLAT ED

  #123 opened 2 years ago by shivUSF
  8

• Not enough memory for BAM sorting

  #122 opened 2 years ago by taot2007
  5

• Annotate Cravat step can not read file

  #121 opened 2 years ago by shivUSF
  12

• HaplotypeCaller - Intervals option

  #118 opened 2 years ago by gremame
  9

• Do I need spliced fastq?

  #120 opened 2 years ago by HyojeenLee
  0

• AWS EC2 + docker and issue of cromwell or STAR

  #119 opened 2 years ago by HyojeenLee
  5

• Could not run the test sample using ctat-mutations

  #111 opened 2 years ago by DecodeGenome
  3

• Localization via hard link has failed:

  #108 opened 3 years ago by vzupan3
  5

• subprocess.CalledProcessError

  #110 opened 2 years ago by min0609
  12

• internet connection error

  #103 opened 3 years ago by jianbiaoli
  5

• CTAT mutations V3.2.0 running error with example data

  #109 opened 2 years ago by hungying
  2

• RNAEditing Analysis

  #107 opened 3 years ago by kokyriakidis
  17

• ctat-mutations-WorkflowFailedState

  #104 opened 3 years ago by taot2007
  5

• File "/opt/conda/lib/python3.7/subprocess.py", line 347, in check_call raise CalledProcessError(retcode, cmd)

  #106 opened 3 years ago by yuanqingyan
  4

• After "WaitingForReturnCode ", pipeline stuck

  #105 opened 3 years ago by jaewon-cho
  4

• question about the outputs

  #102 opened 3 years ago by jaewon-cho
  2

• errors in mutation lib integration

  #101 opened 3 years ago by aoifgri
  5

• Interoperability between CTAT tools

  #100 opened 3 years ago by tjbencomo
  2

• unrecognized parameter name "genomeType" in input "genomeParameters.txt"

  #98 opened 3 years ago by jeongmeani
  1

• information about SNV annotation

  #97 opened 3 years ago by ConcettaDe4
  0

• REDIportal V2.0 update

  #96 opened 3 years ago by kokyriakidis
  1

• error on testing set

  #94 opened 3 years ago by ConcettaDe4
  8

• changing tmp directory of singularity image

  #93 opened 3 years ago by ConcettaDe4
  2

• Terra configuration

  #92 opened 3 years ago by jbeane0428
  1

• EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt"

  #91 opened 3 years ago by jbeane0428
  8

• gatk CreateSequenceDictionary command issue

  #86 opened 4 years ago by readline
  10

• overly verbose Checkpointing info logging msgs

  #88 opened 3 years ago by brianjohnhaas
  0

• EXITING: FATAL INPUT ERROR: unrecognized parameter name "genomeType" in input "genomeParameters.txt"

  #87 opened 4 years ago by YingYa
  3

• needs R installed in Docker for boosting

  #55 opened 4 years ago by brianjohnhaas
  1

• create_report: command not found

  #61 opened 4 years ago by IvantheDugtrio
  4

• Mutations in DEMO data not found

  #81 opened 4 years ago by neoscreen
  5

• UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9

  #80 opened 4 years ago by esebesty
  5

• UnicodeDecodeError: 'utf-8' codec can't decode byte 0xe9 in position 6346: invalid continuation byte

  #60 opened 4 years ago by foxchase
  3

• Supplementary lib doesn't contain gnomad-lite.vcf.gz file and the demo run crashes

  #59 opened 4 years ago by alina-shitrit
  9

• Mutation expected not found

  #56 opened 4 years ago by afaissa
  7

• include PoN

  #54 opened 5 years ago by brianjohnhaas
  0

• optionally add normal dna vcf mask

  #53 opened 5 years ago by brianjohnhaas
  0

• CTAT-mutations-program

  #52 opened 5 years ago by ryangimple
  14

• CTAT-mutation-lib-integration

  #51 opened 5 years ago by ryangimple
  6