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Ensembl/ensembl-vep
Haplosaurus memory and time scaling with vcf

I attempted to use the haplosaurus function to extract protein haplotypes from genome data. Before applying it to my dataset, I tested the function on publicly available VCF files from the 1000 Genomes ...
  • mengysun
  • Opened 
    yesterday
  • #1851

Ensembl/ensembl-vep
VEP does not report gnomAD/1KGP frequencies for some variants with gnomAD/1KGP entries

Describe the issue VEP 113 (with matched cache) seems to be failing to report gnomAD frequencies for some events with gnomAD entries. For instance, the GRCh38 variant chr5:32100960 with REF ATAAG and ...
  • ajw2329
  • 5
  • Opened 
    4 days ago
  • #1850

Ensembl/ensembl-vep
VCF lines with multiple <CNV:TR> ALT alleles get only annotations for the first ALT allele

When an input VCF contain lines with multiple CNV:TR ALT alleles VEP only annotates the first one. (no annotations with ALLELE_NUM 2 or higher present). We would expect annotations for each ALT allele. ...
  • bartcharbon
  • 1
  • Opened 
    8 days ago
  • #1848

Ensembl/ensembl-vep
a case mistake for hgvsp with command line and web

when i input X 154129717 . TCT T , and then hgvsc is NM_000132.4:c.6116_6117del ，hgvsp is - when i input NM_000132.4:c.6116_6117del , and then hgvsc is ENST00000360256.4:c.6116_6117del ...
  • ArsFc
  • 3
  • Opened 
    10 days ago
  • #1847

Ensembl/ensembl-vep
MSG: ERROR: Cache directory --offline/homo_sapiens_refseq not found

Describe the issue I use nextflow to call VEP from conda and find that it always fails to find the path to the cache. But I can run vep fine when I call it alone in terminal. since I want to integrate ...
  • liangxiao023
  • 3
  • Opened 
    15 days ago
  • #1846

Ensembl/ensembl-vep
substr outside of string at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line 917

Describe the issue The following error is produced when trying to process a joint VCF file: substr outside of string at /opt/vep/src/ensembl-vep/Bio/EnsEMBL/Variation/TranscriptVariationAllele.pm line ...
  • suzyhh
  • 2
  • Opened 
    21 days ago
  • #1845

Ensembl/ensembl-vep
ERROR: data file not found for plugins using VEP docker release 113

Dear all, I am contacting you because I cannot make plugins work correctly while running VEP docker. In brief, I pulled the docker image of VEP release 113, and followed the instructions to download ...
  • tettamanzif
  • 3
  • Opened 
    22 days ago
  • #1844

Ensembl/ensembl-vep
Intronic insertion incorrectly assigned an exonic coordinate by VEP 113 (structural variant caller-derived)

Describe the issue VEP generates CDS_position, cDNA_position, and Protein_position values for some intronic insertions. In this example, an insertion falls within a an intron of the USP7 gene. #CHROM ...
  • ajw2329
  • 1
  • Opened 
    29 days ago
  • #1842

Ensembl/ensembl-vep
Installing singularity images of old versions of VEP

Describe the issue Hi there, I am integrating some expression and variant annotation but have realised that the version of Ensembl used for annotation is different between the two data types. I want ...
  • hecrook
  • 2
  • Opened 
    29 days ago
  • #1841

Ensembl/ensembl-vep
VEP does not output motif features (MOTIF_NAME, MOTIF_POS, etc.)

Describe the issue I m doing variant annotation on our WGS data and ran VEP version 112 last summer. Now I updated VEP to version 113 (and respective cache and fasta files) and ran it again on the same ...
  • tuovinent
  • 1
  • Opened 
    on Feb 18
  • #1840
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