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I am trying to run tapes using a vep vcf as input. The vep vcf that I am using as input contains the ClinVar significance information in the CLIN_SIG entry which is part of the CSQ INFO field which ha…
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## Describe the issue
When annotating CNVs with VEP, I get the following error:
```
Illegal division by zero at /media/amontalban/Disc1/VEP/ensembl-vep/modules/Bio/EnsEMBL/VEP/AnnotationSource/Fi…
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Hi,
When I running this command :
`vcf2maf=/data/jiaf/wes_cancer/biosoft/vcf2maf/vcf2maf.pl
vep_path=~/miniconda3/envs/vep/bin/
GENOME=/data/jiaf/wes_cancer/biosoft/gsutil/gatk/hg19/v0/Homo_sapie…
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### Description of the bug
This bug has been around for a while now. When Sarek encounters an error is will often issue the correct error message along with a couple of wrong error messages. The wron…
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Hi dear Ensembl team,
I annotated SNPs/Indels using VEP with cache homo_sapiens_refseq/107_GRCh38. I wanted to calculate the mutation density on regions of CDS, UTR, Intron, IGR and Noncoding,respect…
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### Current Behavior
There may be discrepancies between the annotations generated by the Variant-Linker tool and the VEP online version.
### Proposed Solution
- Select a set of representative…
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Caching VEP annotations (instead of re-running VEP on all variants each time) would speed up the ClinVar pipeline. This would be nice for updating ClinVar data more frequently.
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## Describe the issue
A variant (X:15823107C>CAGCCGG) was not annotated using the gnomADe VCF provided (r2.1.1) by VEP b38. The gnomADe VCF has this variant present with AF=0.0147404 and so should ha…
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Is there a way to pull other annotations from the CSQ field other than the built in INFO.impactful? I see that some of the flags need to be integers or flags, but I have a loftee annotations with "HC"…
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### Description of feature
Currently the workflow uses the VEP cache for annotation, but should also enable using local files from databases for annotation. Hence, other database sources can be added…