konradjk loftee issues - Githubissues

konradjk / loftee

MIT License

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GRCh38 branch does not work in the no root permission OS

#111 Nick-Tan-debug closed 6 days ago
1
gtex.db

#110 BenjaminDEMAILLE opened 1 month ago
2
GRCh38 branch does not work with GRCh37 data

#109 yunkaig opened 5 months ago
0
LOFTEE for CHM13

#108 LuyaoRen opened 5 months 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 ethankreuzer closed 5 months 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 madhushanka opened 6 months ago
0
Loss of END_TRUNC in GRCh38 vs GRCh37 due to change in GERP cutoff from +180 to -58

#105 daniel-wells opened 7 months ago
1
doesn't annotate certain LoF suspected variants?

#104 dtomi0223 opened 7 months ago
0
vep plugin doesnt tag lof variants

#103 roofya opened 1 year ago
1
MSG: Slice start cannot be greater than slice end

#102 xx3411 opened 1 year ago
0
[faidx] Zero length sequence:

#101 jon4thin opened 1 year ago
0
Ancestor files no longer available?

#100 jon4thin closed 1 year ago
1
Use catdir for gerp_bigwig path

#99 dvg-p4 opened 1 year ago
3
Can't exec "samtools"

#98 jxcao98 opened 1 year ago
1
In --tab output format, "PHYLOCSF_TOO_SHORT" shows up in the LoF_info column instead of the LoF_flags column

#97 dvg-p4 opened 1 year ago
0
Suggested GERP bigwig download path is very slow and possibly out-of-date

#96 dvg-p4 opened 1 year ago
1
GERP bigwig file location not concatenated properly

#95 dvg-p4 opened 1 year ago
4
WARNING: Plugin 'LoF' went wrong: Can't locate object method "prepare" via package "false" (perhaps you forgot to load "false"?)

#94 xx3411 opened 1 year ago
3
Loftee VEP plugin creates incorrectly formatted VCFs

#93 pd3 opened 1 year ago
0
fix: use BioPerl instead of Bio::Perl if the latter is not available

#92 Hoeze closed 12 months ago
0
fix: use BioPerl instead of Bio::Perl if the latter is not available

#91 Hoeze closed 12 months ago
0
Error: lib/Bio/DB/BigFile.c: loadable library and perl binaries are mismatched (got handshake key 0xed00080, needed 0xeb00080)

#90 sahwa opened 1 year ago
0
SQL Database not accessible

#89 bethrusnak closed 2 years ago
1
Need to mention in README that master branch has issues with GRCh38

#88 davmlaw closed 1 year ago
2
No splice site and ancestral allele annotations

#87 Filago4 opened 2 years ago
0
Skip calculation of 50_BP_RULE and add NO_EXON_NUMBER flag if framesh…

#86 oleraj closed 2 years ago
7
What is OS in LoF field?

#85 yangyxt closed 3 years ago
1
Merge hg38 branch to master?

#84 Hoeze opened 3 years ago
6
Option gerp_file undocumented

#83 aheinzel opened 3 years ago
0
Use of the option conservation_file mandatory?

#82 aheinzel opened 3 years ago
0
Can loftee apply to other primate species?

#81 KizBaolin opened 3 years ago
0
Loftee results in the ensemble rest api

#80 davidjohngreen opened 3 years ago
0
PhyloCSF database

#79 yinhongwei4079 opened 3 years ago
0
conservation_file

#78 yinhongwei4079 opened 3 years ago
0
if loftee can be used for other species, for example pig

#77 yinhongwei4079 closed 3 years ago
1
Different LoF confidence when adding --fasta option

#76 koido closed 3 years ago
1
Failed to instantiate plugin LoF: Cannot read /vep/loftee/GERP_scores.final.sorted.txt.gz

#75 jielab opened 3 years ago
0
LOFTEE on multi-sample VCF

#74 adinasarapu closed 3 years ago
1
Can't locate object method "prepare" via package "false"

#73 olszewskip opened 4 years ago
10
Failed to compile plugin LoF:Illegal divisions by zero

#72 seunghun23 opened 4 years ago
6
How did gnomAD team process their variants with LOFTEE?

#71 seunghun23 closed 4 years ago
2
Update documentation for hg38?

#70 dantaki closed 4 years ago
1
WARNING: Failed to compile plugin LoF: can't open!

#69 JIBINJOHNV opened 4 years ago
11
Warning: "Use of uninitialized value $faidx"

#68 wuttke closed 4 years ago
2
WARNING: Failed to compile plugin LoF: Attempt to reload Bio/DB/BigFile.pm aborted.

#67 BGI-hys opened 4 years ago
2
conflict between gnomAD and loftee

#66 vserret closed 4 years ago
0
GERP_scores.final.sorted.txt.gz for hg38 ?

#65 Z-Zen closed 4 years ago
0
DBD::SQLite::db prepare failed: no such table: phylocsf_summary

#64 NLSVTN 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 Ninjahelicopter opened 4 years ago
1
Failed to compile plugin LoF: Can't locate List/MoreUtils.pm in @INC

#62 jielab opened 4 years ago
2