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Hello,
there is a problem occurred during the operation. I tried the data of two different patients, one of which was able to run normally, while the other had problems, as shown below:
![Sc…
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## Describe the issue
As mentioned in https://github.com/Ensembl/ensembl-vep/issues/566, INSTALL.pl's update (and check-for-update) procedures use the GitHub REST API, and thus are susceptible to f…
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## Describe the issue
We investigated how vep annotates inversions and performed an inversion in the vcf file on the region chr17:7671525-7685229, where vep was expected to assign a HIGH impact to th…
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Hello,
I applied `vcf2maf` to a vcf file cleaned with `vcf2vcf`. The original vcf was an output from `pindel`. I have the following error from running `vcf2maf`.
Would you please help me to succe…
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The code currently gives this warning:
```
/fh/fast/bloom_j/software/miniconda3/envs/dms-vep-pipeline/lib/python3.11/site-packages/dms_variants/codonvarianttable.py:1779: FutureWarning: In a future …
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### Which type of feature are you implementing?
- [X] I have selected (at least) one of the following `Label` for the feature
### Is there an existing issue / PR for this?
- [X] I have searched for…
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### Description of feature
There appears to be some tentative user interest for the Genomenon Mastermind - see [this thread](https://github.com/Clinical-Genomics/scout/issues/4020). VEP has a plugin
…
dnil updated
4 months ago
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Hi, I am trying to use LOFTEE on my VEP (v101), and when I ran it, I got following error messages
Smartmatch is experimental at /cromwell_root/fc-e734351b-f1b6-4677-a5c8-efe72c774013/Reference_fil…
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I have a problem with VEP it seems. Complaining about Unknown option: af_gnomad
perl ~/software/vcf2maf-1.6.21/vcf2maf.pl --ref-fasta /home/local/xxxx/.vep/homo_sapiens/102_GRCh38/Homo_sapiens.…
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Currently, the ensembl-vep recipe installs the LOFTEE plugin:
https://github.com/bioconda/bioconda-recipes/blob/125fda88b74141df9c8482ce96254aaf72e6c81b/recipes/ensembl-vep/build.sh#L46-L54
Unfortun…
Hoeze updated
2 years ago