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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Q: How to filter variants by a specific feature before --pick_order is applied?

#1711 asalimih closed 1 day ago
5
VEP112 predicts "inframe_insertion, stop_retained_variant" in cases where previously was predicted as "frameshift_variant, stop_gained"

#1710 jperales opened 2 days ago
3
Fix option individual_zyg

#1709 dglemos opened 2 days ago
0
Cant Install plugins

#1708 GianlucaMattei closed 1 day ago
4
Input full path to cache directory

#1707 nuno-agostinho opened 3 days ago
0
Skip adding EMER regulatory feature in VEP cache

#1706 nakib103 closed 2 days ago
0
Synonyms file does not work in the offline mode

#1705 XinmengLiao opened 1 week ago
2
CDS coordinate misalignment for some genes in VEP version 112

#1704 GSYongWu opened 1 week ago
2
--individual_zyg ind or all option triggers error.

#1703 schreyers opened 1 week ago
15
Avoid installing Coveralls in Travis CI for Perl 5.10

#1702 nuno-agostinho closed 4 days ago
1
Fix filtering of RefSeq transcripts in mitochondria

#1701 nuno-agostinho closed 4 days ago
0
Fix warning when using SV in VCF format with 5 fields

#1700 nuno-agostinho closed 4 days ago
0
Supporting Gencode primary

#1699 likhitha-surapaneni opened 2 weeks ago
0
VEP v112 `ALLELE_NUM` empty in output VCF for input SV

#1698 dennishendriksen closed 4 days ago
11
gnomAD r4.1.0 for G2P

#1697 MikeHala opened 2 weeks ago
1
Different cDNA length for several RefSeq transcript

#1696 barbarian1803 closed 1 week ago
2
Missing genes on chrMT when using --refseq

#1695 ju-mu closed 2 weeks ago
3
VEP error for structural variation VCF input

#1694 barbarian1803 opened 3 weeks ago
2
Docker v111.0 and. v112.0 got error bgzip not found in path

#1693 barbarian1803 closed 3 weeks ago
3
Use extracted data against of compressed [QUESTION]

#1692 GhorbaniAli opened 3 weeks ago
1
From which COSMIC donwlodad file do the "Existing_variation" come?

#1691 MGCarta opened 3 weeks ago
2
VEP installer not downloading cache files when specified

#1690 ethankreuzer opened 3 weeks ago
1
Update delimiter for FILTER when used for custom option

#1689 nakib103 closed 3 weeks ago
0
VCF FORMAT field output in --tab

#1688 NotAPoetButACriminal opened 3 weeks ago
6
Allow passing a github token to avoid rate limit errors

#1687 dvg-p4 opened 4 weeks ago
1
--exclude_predicted

#1686 jammywwh closed 2 weeks ago
4
VEP custom outputs coordinates of the annotation by adding +1 to start position in Structural Variants

#1685 jperales closed 3 weeks ago
3
Possible bug with flag_pick_allele

#1684 GACGAMA opened 1 month ago
5
1000 genomes project custom annotation Issue

#1683 CASTANYMIQUEL closed 1 month ago
2
VEP 88: Update Dockerfile to build VEP 88.14

#1682 nuno-agostinho opened 1 month ago
2
Performance and Error Issues with VEP v111 Docker Container

#1681 Ananya-swi opened 1 month ago
4
Differing ClinVar clinical significance annotation according to transcript/feature

#1680 growland2 opened 1 month ago
2
No annotation results from plugins using Singularity

#1679 yotsa opened 1 month ago
3
Add slurm configuration for DumpVEP pipeline

#1678 nakib103 closed 2 weeks ago
0
Patching test databases

#1677 likhitha-surapaneni closed 2 weeks ago
0
Clarification Needed on dbNSFP Plugin Annotation for Variants with Multiple Values

#1676 sibylZHAI closed 1 month ago
2
Nextflow: Accept and split non-VCF input formats

#1675 nuno-agostinho closed 3 weeks ago
0
--safe option seems broken

#1674 bartcharbon opened 1 month ago
2
Allow filtering in nextflow-vep

#1673 nakib103 closed 1 month ago
0
NAN allele encoding in JSON output

#1672 muppetjones opened 1 month ago
1
VEP Installation Failed: Failed 2/42 test programs. 0/1752 subtests failed.

#1671 Lukecassar21 opened 1 month ago
4
Fix unit test with updated incompatibility list

#1670 nakib103 closed 1 month ago
0
Keep values from input INFO column in output

#1669 schreyers closed 1 month ago
7
Stop_gained not reported

#1668 KevinMer closed 1 month ago
4
Failed to instantiate plugin dbNSFP: ERROR: Could not retrieve dbNSFP version from filename

#1667 yougulianren closed 1 week ago
2
docker run issue and pm module missing

#1666 vyomesh4bcOnco opened 2 months ago
9
Nextflow Failing with Missing Output File

#1665 sharra44 closed 2 months ago
9
Alternative allele of matched variants is not reported in custom annotation with overlap method

#1664 jperales opened 2 months ago
1
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