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konradjk
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loftee
MIT License
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gtex.db
#110
BenjaminDEMAILLE
opened
2 days ago
2
GRCh38 branch does not work with GRCh37 data
#109
yunkaig
opened
3 months ago
0
LOFTEE for CHM13
#108
LuyaoRen
opened
3 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
4 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
4 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
5 months ago
1
doesn't annotate certain LoF suspected variants?
#104
dtomi0223
opened
5 months ago
0
vep plugin doesnt tag lof variants
#103
roofya
opened
11 months 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
11 months 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Suggested GERP bigwig download path is very slow and possibly out-of-date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
10 months ago
0
fix: use BioPerl instead of Bio::Perl if the latter is not available
#91
Hoeze
closed
10 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
2 years ago
1
Merge hg38 branch to master?
#84
Hoeze
opened
2 years ago
6
Option gerp_file undocumented
#83
aheinzel
opened
2 years ago
0
Use of the option conservation_file mandatory?
#82
aheinzel
opened
2 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
3 years ago
10
Failed to compile plugin LoF:Illegal divisions by zero
#72
seunghun23
opened
3 years ago
6
How did gnomAD team process their variants with LOFTEE?
#71
seunghun23
closed
3 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
Loftee doesn't support parallel processing with VEP --fork argument (unobvious MySQL error)
#61
rostkick
opened
4 years ago
1
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