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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Failing tests `t/Runner.t`

#1802 PetrKralCZ opened 13 hours ago
1
missing novel transcript in the VEP output

#1801 tuncayseker opened 1 day ago
1
Annotation fails randomly with structural variants coming from Manta

#1800 fperezcobos opened 5 days ago
6
Indel Annotation Problem with Uploaded Variation Column

#1799 hkirmak closed 10 hours ago
10
Annotation fails if contigs has no annotations in gtf

#1798 fperezcobos closed 4 days ago
0
Force set --offline if no database setup

#1797 nakib103 opened 6 days ago
0
Incorrect Annotation for Frameshift Variant in VEP 113

#1796 GSYongWu opened 6 days ago
7
Patching all test DBs to 114

#1795 nakib103 closed 6 days ago
0
Add new option to fetch clinvar somatic classification + patch db for 115

#1794 dglemos opened 1 week ago
1
Annotation Discrepancy for Variant 1:98348885_G>A in VEP 113

#1793 GSYongWu opened 1 week ago
5
Homo_sapiens.GRCh38.dna.toplevel.fa.gz.fai file not updated in release 113

#1792 rklocke opened 1 week ago
0
vep can't find index file

#1791 jerrypgreenberg opened 1 week ago
3
Missing annotation of intergenic region, --distance doesn't help

#1790 dshafranskaya opened 1 week ago
0
Fix tests for get_end

#1789 likhitha-surapaneni closed 5 days ago
0
Fix transcript mismatch warning message

#1788 dglemos closed 6 days ago
3
VEP 113 Interrupts on Large VCF Files with Numerous Transcript-assembly Mismatch Warnings

#1787 GSYongWu opened 2 weeks ago
4
No protein version from overlap/id/:id end point results

#1786 XLIU-hub opened 2 weeks ago
1
Issue with Adding Custom BED File to Ensembl VEP as a Coverage Database

#1785 mrymkdnz opened 2 weeks ago
1
VEP needs sorted VCFs again

#1784 gernophil opened 2 weeks ago
1
Unable to Locate PolyPhen and SIFT SQLite Files for CHM13 Genome

#1783 LuyaoRen opened 3 weeks ago
1
How to filter the annotated result for each variant?

#1782 Xi-Cao closed 2 weeks ago
13
VEP can't handle gzipped vcf as input

#1781 Lloyd-LiuSiyi closed 2 weeks ago
8
Multiple CSQ fields when re-annotating a VCF with --keep_csq

#1780 TimD1 closed 10 hours ago
2
ONE-BASED REFERENCE

#1779 vappiah opened 1 month ago
1
Bugfix: division by zero in overlaps

#1778 nakib103 closed 2 weeks ago
0
VEP progress bar

#1777 nihalraman closed 1 month ago
2
Fix end position for SV insertion types

#1776 nakib103 closed 3 weeks ago
1
MSG: The coordinate interval for display is of different length than for the reference allele

#1775 suzyhh opened 1 month ago
7
Missing annotations for BND variants.

#1774 ramprasadn opened 1 month ago
2
Downstream changes for get_end fix in VCF parser

#1773 nakib103 closed 2 weeks ago
0
VCF OUTPUT NOT VALID

#1772 vappiah closed 1 month ago
2
checksum for <genome> doesn't match checksum in CHECKSUMS file on FTP site

#1771 amizeranschi opened 1 month ago
2
Remove dependency on non indexed cache

#1770 likhitha-surapaneni opened 1 month ago
0
Optimize WGS VCF File Annotation for Improved Performance and Speed

#1769 Ananya-swi opened 1 month ago
7
How can I use my own fasta and gff to annotate?

#1768 DayTimeMouse opened 1 month ago
1
MSG: ERROR: No such operator "D"

#1767 BenjaminDEMAILLE opened 1 month ago
1
Question: Is it normal to get multiple values in the output from the FORMAT for GT:GQ:AD:DP:VF etc?

#1766 schreyers closed 1 month ago
3
Error division by zero

#1765 xsoleacha closed 2 weeks ago
3
`substr outside of string` in VariationEffect.pm line 1329

#1764 bartgrantham opened 1 month ago
6
VEP REST API - Variation allele parameter

#1763 vappiah closed 1 month ago
3
Parse gene and transcript version from GFF/GTF file

#1762 nakib103 closed 1 month ago
0
Can't use filter_vep subfields in the tab separated vep output file

#1761 tamil-acog closed 3 weeks ago
3
Variants on chrY are annotated with genes located on chrX (non-PAR region)

#1760 bartcharbon closed 1 month ago
1
Inconsistent HGNC:ID results between single-thread and multi-thread in vep

#1759 karlestira opened 2 months ago
6
Remove deprecated funcgen function

#1758 nakib103 closed 1 month ago
0
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 10 hours ago
5
nextflow-vep: output_prefix can be null when used from workflow

#1753 nakib103 closed 1 month ago
0