konradjk/loftee

Issues

• GRCh38 branch does not work with GRCh37 data

  #109 opened 10 days ago
  0

• LOFTEE for CHM13

  #108 opened 17 days ago
  0

• WARNING: Failed to compile plugin LoF: Can't locate Bio/DB/BigWig.pm in @INC (you may need to install the Bio::DB::BigWig module)

  #107 opened a month ago
  0

• WARNING: Plugin 'LoF' went wrong: Undefined subroutine &LoF::reverse_complement called at $CONDA_PREFIX/share/ensembl-vep-111.0-0/LoF.pm line 491

  #106 opened a month ago
  0

• Loss of END_TRUNC in GRCh38 vs GRCh37 due to change in GERP cutoff from +180 to -58

  #105 opened 2 months ago
  1

• doesn't annotate certain LoF suspected variants?

  #104 opened 3 months ago
  0

• vep plugin doesnt tag lof variants

  #103 opened 8 months ago
  1

• MSG: Slice start cannot be greater than slice end

  #102 opened 10 months ago
  0

• [faidx] Zero length sequence:

  #101 opened a year ago
  0

• Ancestor files no longer available?

  #100 opened 9 months ago
  1

• Can't exec "samtools"

  #98 opened a year ago
  1

• In --tab output format, "PHYLOCSF_TOO_SHORT" shows up in the LoF_info column instead of the LoF_flags column

  #97 opened a year ago
  0

• Suggested GERP bigwig download path is very slow and possibly out-of-date

  #96 opened a year ago
  1

• GERP bigwig file location not concatenated properly

  #95 opened a year ago
  4

• WARNING: Plugin 'LoF' went wrong: Can't locate object method "prepare" via package "false" (perhaps you forgot to load "false"?)

  #94 opened a year ago
  3

• Loftee VEP plugin creates incorrectly formatted VCFs

  #93 opened a year ago
  0

• Error: lib/Bio/DB/BigFile.c: loadable library and perl binaries are mismatched (got handshake key 0xed00080, needed 0xeb00080)

  #90 opened a year ago
  0

• SQL Database not accessible

  #89 opened 2 years ago
  1

• Need to mention in README that master branch has issues with GRCh38

  #88 opened a year ago
  2

• No splice site and ancestral allele annotations

  #87 opened 2 years ago
  0

• What is OS in LoF field?

  #85 opened 3 years ago
  1

• Merge hg38 branch to master?

  #84 opened 3 years ago
  6

• Option gerp_file undocumented

  #83 opened 3 years ago
  0

• Use of the option conservation_file mandatory?

  #82 opened 3 years ago
  0

• Can loftee apply to other primate species?

  #81 opened 3 years ago
  0

• Loftee results in the ensemble rest api

  #80 opened 3 years ago
  0

• PhyloCSF database

  #79 opened 3 years ago
  0

• conservation_file

  #78 opened 3 years ago
  0

• if loftee can be used for other species, for example pig

  #77 opened 3 years ago
  1

• Different LoF confidence when adding --fasta option

  #76 opened 3 years ago
  1

• Failed to instantiate plugin LoF: Cannot read /vep/loftee/GERP_scores.final.sorted.txt.gz

  #75 opened 3 years ago
  0

• LOFTEE on multi-sample VCF

  #74 opened 4 years ago
  1

• Can't locate object method "prepare" via package "false"

  #73 opened 4 years ago
  10

• Failed to compile plugin LoF:Illegal divisions by zero

  #72 opened 4 years ago
  6

• How did gnomAD team process their variants with LOFTEE?

  #71 opened 4 years ago
  2

• Update documentation for hg38?

  #70 opened 4 years ago
  1

• WARNING: Failed to compile plugin LoF: can't open!

  #69 opened 4 years ago
  11

• Warning: "Use of uninitialized value $faidx"

  #68 opened 4 years ago
  2

• WARNING: Failed to compile plugin LoF: Attempt to reload Bio/DB/BigFile.pm aborted.

  #67 opened 4 years ago
  2

• conflict between gnomAD and loftee

  #66 opened 4 years ago
  0

• GERP_scores.final.sorted.txt.gz for hg38 ?

  #65 opened 4 years ago
  0

• DBD::SQLite::db prepare failed: no such table: phylocsf_summary

  #64 opened 4 years ago
  0

• Failed to instantiate plugin LoF: Can't open /vep/loftee/splice_data/donor_motifs/ese.txt: No such file or directory at /home/.vep/Plugins/loftee_splice_utils.pl line 212

  #63 opened 4 years ago
  1

• Failed to compile plugin LoF: Can't locate List/MoreUtils.pm in @INC

  #62 opened 5 years ago
  2

• Loftee doesn't support parallel processing with VEP --fork argument (unobvious MySQL error)

  #61 opened 5 years ago
  1

• WARNING: Failed to compile plugin LoF: can't open!

  #60 opened 5 years ago
  2

• Fail to instantiate plugin LoF

  #59 opened 5 years ago
  1

• Unable to use Loftee plugin from grch38 branch

  #58 opened 4 years ago
  5

• LofTee releases - grch37 vs. grch38

  #56 opened 5 years ago
  4

• fail to run plugin LoF

  #55 opened 5 years ago
  0