Ensembl ensembl-vep issues

Ensembl / 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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issues

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VEP runs but resulting VCF contains no VEP annotated records when trying to annotate variants using T2T assembly

#1757 indapa closed 2 months ago
2
Update gnomad v4.1 sub populations in relevant places

#1756 nakib103 closed 2 months ago
1
Can not find .index file for FASTA file

#1755 kuaileshizuihao opened 2 months ago
4
gnomADe annotation not presented for a variant

#1754 Aisha-D closed 4 days ago
5
nextflow-vep: output_prefix can be null when used from workflow

#1753 nakib103 closed 1 month ago
0
Use of uninitialized value warning issued by plugins/Conservation.pm

#1752 rraadd88 closed 2 months ago
2
Do not install Devel::Cover if perl version is 5.10

#1751 nakib103 closed 2 months ago
0
Fix inconsistencies between --hgvs and --hgvsg

#1750 nuno-agostinho closed 2 months ago
0
Nextflow: add parameter to specify VEP version

#1749 nuno-agostinho closed 2 months ago
1
Docker: Raise error if VEP version and release branch mismatch

#1748 nuno-agostinho closed 2 months ago
0
negative repeat count does nothing at quantifier.pl line 1312, <in> line 5603.

#1747 erickfabian0 closed 2 months ago
2
G2P for "BOTH monoallelic and biallelic" genes in PanelApp panels

#1746 MikeHala closed 2 months ago
2
Paralogues plugin: install ensembl-compara

#1745 nuno-agostinho closed 3 months ago
1
Capture uploaded allele correctly for VCF input

#1744 likhitha-surapaneni opened 3 months ago
0
Update nextflow config

#1743 veidenberg closed 3 months ago
0
incomplete html stats files

#1742 zyxNo1 closed 2 months ago
2
HGVS C dot not using right most aligned option

#1741 namiller2015 closed 1 month ago
7
Custom bigwig annotation not working for insertion variants

#1740 asalimih closed 3 months ago
9
Fixing filter when value is hash and contains text and number

#1739 likhitha-surapaneni closed 3 months ago
1
Check extension also when deciding runVEPonVCF process

#1738 nakib103 closed 3 months ago
0
Tiny bugfix

#1737 veidenberg closed 3 months ago
1
Quick fix to improve warnings

#1736 likhitha-surapaneni closed 3 months ago
0
Update slurm profile and resource limits

#1735 veidenberg closed 3 months ago
3
Improving --gencode_primary and --flag_gencode_primary

#1734 likhitha-surapaneni closed 3 months ago
0
Add pick_count option - number of results to return by pick

#1733 nakib103 opened 3 months ago
0
High memory usage due to 368 BRCA1 RefSeq transcripts - Transcript blocklist / allowlists or option for max transcripts

#1732 davmlaw opened 4 months ago
3
Document --max_sv_size command line default

#1731 davmlaw closed 3 months ago
2
ERROR: Can't detect input format

#1730 Zhang-Rui-2018 closed 4 months ago
2
Updating release related files

#1729 likhitha-surapaneni closed 4 months ago
0
VEP installation can not install Bio::DB:HTS module

#1728 xiyasong closed 3 months ago
2
DumpVEP: fix QC step for using non-reference sequence

#1727 nakib103 closed 4 months ago
0
SpliceAI plugin update please

#1726 xiucz closed 3 months ago
1
Include gencode primary in transcript attrib list for dumper pipeline

#1725 likhitha-surapaneni closed 4 months ago
0
Nextflow VEP: support Seqera platform

#1724 nuno-agostinho closed 3 months ago
0
filter_vep on HGNC_ID

#1723 fellen31 closed 3 months ago
5
Request for Documentation and Containerization of Bio::EnsEMBL::XS Module for VEP to run faster.

#1722 JoshuaSWIBI closed 3 months ago
3
Seeking clarity on --fields vs --custom usage

#1721 errcricket closed 4 months ago
4
VEP 88 Docker: Create docker.yml worfklow

#1720 nuno-agostinho closed 4 months ago
0
issue specifiying cache dir (-d) and downloading files

#1719 errcricket closed 4 months ago
2
Fix missing non reference seq region in VEP cache

#1718 nakib103 closed 4 months ago
0
Allow to add version to gene stable id

#1717 nakib103 closed 4 months ago
0
"No cache found for homo_sapiens, version 105", but the latest version is 112

#1716 jielab closed 2 months ago
6
StructuralVariantOverlap Hanging Indefinitely

#1715 ghost closed 3 months ago
2
`0` does not work as a variant identifier

#1714 dvg-p4 closed 4 months ago
3
Transcript-assembly mismatch refseq annotation - print warning

#1713 dglemos closed 3 months ago
1
Add gnomAD v4.1 populations

#1712 nakib103 closed 4 months ago
0
Q: How to filter variants by a specific feature before --pick_order is applied?

#1711 asalimih closed 5 months ago
5
VEP113 & VEP112 predict "inframe_insertion, stop_retained_variant" in cases where previously was predicted as "frameshift_variant, stop_gained"

#1710 jperales opened 5 months ago
8
Fix option individual_zyg

#1709 dglemos closed 5 months ago
1
Cant Install plugins

#1708 GianlucaMattei closed 5 months ago
4

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