-
Hi,
I am trying to use loftee plugin (Grch38) as a part of VEP and I got the following error.
Could you please help?
Thanks in advance
**Command used**
docker run -t -i -v /home/vep_data/:/…
-
Hello,
I wanted to check if a plugin for ensembl_vep tool (already in Galaxy) could be added to te tool: **nmd** or nonsense mediated decay which predicts whether a transcript escapes the nonsense me…
-
### 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…
-
### 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…
-
I encountered error below:
Script:
```
perl vcf2maf.pl --input-vcf tests/test.vcf --output-maf tests/test.vep.maf --ref-fasta $ref
```
Error message:
```
[W::fai_get_val] Reference 13:2860…
-
-
### Description of the bug
After the recent update of the module [bea3ca9](https://github.com/nf-core/modules/commit/bea3ca998816a7f812b1bbbcb27c3a9ffbac0706), `ENSEMBLVEP` process fails:
```
-…
-
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…
-
The genome-nexus-vep supports retrieving VEP annotations by a list of variants in **ENSEMBL region** format only.
There is no endpoint to do it by a list of variants in **hgvs** format at the moment.…
-
When exploring the cross validation tables (50 iteration table) - specifically TP53 BRCA - I found a mutation that is not annotated with any of the consequence type we expect:
| chr | pos | ref | a…