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Ensembl
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ensembl-vep
The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants
https://www.ensembl.org/vep
Apache License 2.0
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the web file has no image
#1663
fan040
opened
2 months ago
5
WARNING: Chromosome ? not found in annotation sources or synonyms on line ?
#1662
jooY-Jeong
closed
2 months ago
2
Different output results between only used chm13v2.0_GENCODEv35_CAT_Liftoff.vep.gff3.gz and used chm13v2.0_GENCODEv35_CAT_Liftoff.vep.gff3.gz with other database
#1661
yougulianren
opened
2 months ago
5
You must specify a region in the format chr, chr:start or chr:start-end at perl5/5.32/site_perl/Bio/DB/HTS/Tabix.pm line 104
#1660
xmy1990
closed
2 months ago
3
Outdated or missing genes when using RefSeq cache
#1659
gabrielhim
opened
2 months ago
5
Homo Sapiens GRCH38 Merged Cache Installation Failing on CHECKSUMS
#1658
sharra44
closed
2 months ago
10
Can't locate Bio/EnsEMBL/Utils/Exception.pm in @INC
#1657
jooY-Jeong
closed
2 months ago
2
Use of uninitialized value at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/IO/Parser/GTF.pm
#1656
RanWei1987
closed
2 months ago
4
Haplo results interpratation
#1655
Jokendo-collab
opened
2 months ago
1
VEP version 111 outputs HGVSp duplications not following the 3' rule in regions of repeated aminoacids
#1654
jperales
closed
1 month ago
2
VEP version 112 outputs HGVSg substitution instead of deletion for one out of the two alternative allele deletions
#1653
jperales
opened
2 months ago
8
output HGVSp nomenclature is non-standard
#1652
sunhuaibo
closed
1 month ago
2
Using one of the two annotation sources VCF is used when same annotation source name is used
#1651
Aisha-D
opened
2 months ago
5
Need to add sample specific genotype information to the data frame generated using VEP annotated vcf file.
#1650
AppWick-hub
opened
2 months ago
13
dbNSFP plugin not getting results for specified columns
#1649
aruta321
closed
2 months ago
14
VEP VCF output
#1648
Azjer2014
closed
2 months ago
0
Normalization of VCF file
#1647
celine-weng
closed
1 week ago
2
Custom VCF w/overlap joins multiple FILTER values for a record with same delimiter ("&") as other records
#1646
davmlaw
closed
2 weeks ago
2
Feature Requests for custom VCF to be able to retrieve both ID and coords (to replace StructuralVariantOverlap)
#1645
davmlaw
opened
3 months ago
2
`--mirna` not providing results for RefSeq transcript source
#1644
dennishendriksen
opened
3 months ago
2
Remove redundant symbolic alt to so term hash
#1643
nakib103
opened
3 months ago
0
Fix incompatibility
#1642
nakib103
closed
2 months ago
2
INSTALL.pl - Switch to https?
#1641
sjaenick
opened
3 months ago
3
WARNING: Chromosome chr3_GL000221v1_random not found in annotation sources or synonyms; chromosome chr3_GL000221v1_random does not overlap any features
#1640
bobojin46
closed
1 week ago
12
INSTALL.pl -f GRCh37 fasta not bgzipped
#1639
davmlaw
opened
3 months ago
3
Gnomad custom annotation vcf-format
#1638
karoliinas
opened
3 months ago
4
Improper calculation of SV size for SVs cross different chromosomes
#1637
gudeqing
opened
3 months ago
3
Fix SVTYPE when using IUPAC nucleotide codes
#1636
nuno-agostinho
closed
2 months ago
1
NCBI Fasta causing somewhat arbitrary renaming of chromosomes and thus silent dropping of plugin annotations
#1635
davmlaw
closed
2 months ago
3
SIFT score source
#1634
jonahcullen
closed
2 months ago
8
HGVS notation for dup in 109 becomes ins in 110
#1633
barbarian1803
opened
3 months ago
4
Problem of: Use of uninitialized value
#1632
celine-weng
closed
3 months ago
5
Annotation skipped due to `type is not supported` error for certain manta indels
#1631
alkc
closed
1 month ago
4
Can't locate DBI.pm in @INC
#1630
sagitaninta
closed
3 months ago
2
Docker 112 release doesn't build
#1629
Artemlin6231
closed
1 week ago
2
Mismatch between cache and assembly for T2T
#1628
Heather1999
closed
1 week ago
12
Support NCBI microbe annotation with no transcripts (CDS only)
#1627
nuno-agostinho
opened
3 months ago
0
Fix unit test for e113
#1626
nuno-agostinho
closed
2 months ago
0
Remove problematic unit test
#1625
nuno-agostinho
closed
2 months ago
1
trouble finding cache file "MSG: ERROR: Cache directory /..."
#1624
waaaliceee
closed
2 months ago
7
VEP in Google Batch fails when more than 5 custom databases are passed
#1623
MatteoSchiavinato
closed
4 months ago
6
WARNING: Chromosome 22 not found in annotation sources or synonyms on line 1
#1622
MaayanYoles
closed
4 months ago
8
filter_vep output file larger than input file
#1621
sdhutchins
opened
4 months ago
2
All variants are intergenic with NCBI GFF
#1620
dzc0104
opened
4 months ago
8
Improve statistics output
#1619
nuno-agostinho
closed
2 months ago
1
Fix SV warnings for short variants in `region` format
#1618
nuno-agostinho
closed
3 months ago
1
False warning messages with vep 111 when using the range input format
#1617
ju-mu
closed
3 months ago
4
Normalisation-based allele matching algorithm and custom file
#1616
KevinMer
closed
4 months ago
2
can not call method "seq"
#1615
Marije179
opened
4 months ago
6
Export newly moved function to different module
#1614
nakib103
closed
4 months ago
1
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