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## Describe the issue
Since vep105 added new splice region variant annotations (i.e., splice_donor_region_variant, splice_donor_5th_base_variant, splice_polypyrimidine_tract_variant), variants that w…
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Hi,
I was just wondering how the _make_snpfile.py_ deals with annotations in different transcripts/genes of the same variation. Does the script only take into account only the first instance of the …
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When using RefSeq merged cache for GRCh37, VEP returns outdated symbols of some genes, even though the same genes are reported with the updatd symbol in RefSeq GFF.
For instance, genes IKBKAP and D…
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Hello,
For the following variant in VCF format
`chr19 1219320 . CACGTATATG CCCG`
This represents a variant that looks like this
`CACGTATATGGTG REF
CCCG--------GTG ALT`
We hav…
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Hello there,
My file was annotated using VEP, and I am trying to convert the annotated VEP output to a format accepted by VPOT.py using these commands:
python3 ../VPOT_6_1_convertVEP.py utility …
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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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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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Currently, we do a get_or_create in here ```annotation.annotation_versions.get_variant_annotation_version``` which is triggered by visiting annotation pages
Better to do in management command and/or …
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## Describe the issue
We noticed a variant, a single base insertion after the first position of a gene, getting annotated as an upstream_gene_variant with respect to that gene. The distance is then…
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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…