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## Describe the issue
When filtering using `./filter_vep`, the same behaviour from `vep --transcript_filter` does not seem possible.
When running vep and directly filtering on a defined number of …
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Hello,
I am using VEP 104.3, cache homo_sapiens_vep_104_GRCh38, latest version of everything including the dbNSFP plugin, and dbNSFP v4.2a .
When a VCF row has multiple ALT alleles listed, the dbN…
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Sarah says: I think we need to look at VEP pick order for refseq - currently choosing the wrong transcripts for a bunch of really important genes (e.g. NR for BRCA1, SCN1A etc), can't see us being ab…
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Hi there,
I am wondering whether it is possible to run vep with reference genome not in the database?
(the reference genome has an annotation file)
Best
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https://scout.scilifelab.se/cust002/F0037125/cce4d3ad01f80405137e886f6b26f519
The position in transcript HGNC NM_022089 should be c.2978 not as below, which is shown in Scout.
| ATP13A2 | NM_0…
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thanks a lot
* pvactools version:latest
* Python version:3.7
* Operating System:centos
**Describe the bug**
Failed to compile plugin Wildtype: Excessively long operator at /data/database/anno/…
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## Describe the issue
when using GFF/GTF transcript annotations as an annotation source, the VEP cannot proceed.
Error:
Can't locate object method "new" via package "Bio::EnsEMBL::VEP::Annotation…
ghost updated
3 years ago
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## Describe the issue
A clear and concise description of what the bug is.
## Additional information
Please fill in the following sections to help us find the source of your issue as quickly as po…
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Add protein domains (from VEP annotations) to variant page.
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**Describe the bug**
I am unable to view HGVS annotations for variants (I've never been able to since installing local seqr version). I've dumped psql references databases and recreated to check that…