cancerit/VAGrENT

Issues

• Additional classification shortcut

  #44 opened 3 years ago by AndyMenzies
  0

• Admin_EnsemblReferenceFileGenerator.pl not producing any result for a list of transcripts

  #41 opened 4 years ago by nvolkovaGEL
  7

• system() doesn't trigger try/catch, needs autodie or actual test of return variable

  #39 opened 5 years ago by keiranmraine
  3

• -o option should not append .gz if already present

  #38 opened 5 years ago by keiranmraine
  0

• Speed up with in memory interval trees

  #35 opened 5 years ago by keiranmraine
  0

• Building cache files

  #32 opened 5 years ago by gbnci
  7

• Documentation out of line with new release (3.3.0)

  #30 opened 6 years ago
  1

• Assumes write on exec location

  #33 opened 5 years ago by keiranmraine
  0

• SO numbers inserted into VC field

  #31 opened 6 years ago by JocelynSP
  2

• Build Cache for Ensembl 91 and GRCh37

  #27 opened 7 years ago by jsmedmar
  9

• bedtools in setup.sh

  #29 opened 7 years ago by keiranmraine
  0

• Remove shell out for samtools faidx

  #24 opened 7 years ago by keiranmraine
  0

• Issue in ensembl data import admin scripts - Some CCDS transcripts missed

  #5 opened 7 years ago by AndyMenzies
  1

• Allow local paths to ensembl GTF and fasta files in cache creation scripts

  #13 opened 7 years ago by AndyMenzies
  2

• v3.2.3 Fails to compile

  #26 opened 7 years ago
  6

• Unstable annotation deletions and complex

  #25 opened 7 years ago by keiranmraine
  1

• vcf-sort not sufficient for indel

  #23 opened 7 years ago by keiranmraine
  0

• bedtools reqiured but not indicated

  #22 opened 7 years ago by keiranmraine
  1

• Ontology assignment bug, upstream/downstream variants being labelled as UTR.

  #1 opened 7 years ago by AndyMenzies
  1

• Unable to run Admin_GeneRegionBedDumper.pl

  #18 opened 8 years ago by sb43
  3

• Admin_EnsemblReferenceFileGenerator.pl - poor error messages

  #15 opened 8 years ago by keiranmraine
  0

• Admin_EnsemblReferenceFileGenerator.pl - empty or corrupt cache file

  #17 opened 8 years ago by keiranmraine
  0

• Bareword errors in test runs

  #14 opened 9 years ago by keiranmraine
  1

• Complex-variant vcf spec interpretation

  #12 opened 9 years ago by jwhsanger
  0

• Dependency on non-standard INFO 'LEN' field for annotating complex indels

  #10 opened 9 years ago by jwhsanger
  2

• Crash bug in Admin_GeneRegionBedDumper.pl

  #6 opened 9 years ago by AndyMenzies
  0

• Crash bug in Admin_EnsemblReferenceFileGenerator.pl - crashes out trying to process Ensembl 80 human

  #7 opened 9 years ago by AndyMenzies
  0

• UTR Splice changes anchored to first/last base of the CDS only getting RNA annotation

  #4 opened 9 years ago by AndyMenzies
  1