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## Describe the issue
when using transcript annotations defined in GFF file, VEP performed incorrect HGVS.p annotation for the variant chr10:87754701-CAT-C,NM_032810.4:c.1070_1071del (rs751499706)
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## Describe the issue
Hello,
I'm currently using custom annotation to retrieve upstream variant annotation.
My custom annotation is a clinvar vcf that I processed to add p. informations from NCB…
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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
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dnil updated
2 months ago
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allow user to select content type to return vep annotations in
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Hi,
We are currently using the VEP v111 Docker container to annotate VCF files. However, we are facing the following issues:
1. Performance Issue: Annotation of a very small sample VCF file takes…
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**Is your feature request related to a problem? Please describe.**
Both VEP and open-cravat support plugins, which can extend annotation capabilities without requiring these to be directly integrated…
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### Description of the bug
Hi,
The pipeline is executing succesfully until the end but skip annotation processes despite params.annotate_tool is not null. I tried to set it up with 'vep' and 'merg…
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VEP: http://uswest.ensembl.org/info/docs/tools/vep/index.html
Similar to the SnpEff annotation we have already, VEP is a tool to compute variant impact.
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The files are all existing and in correct folder structure after I moved them. Now when I run `cwl-runner --validate` I get this error below and `org.w3id.cwl.cwl.File` is no where in this yml file.
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Based on the findings of the DDD paper, we would like to be able to filter for the following variant annotations created by the VEP SpliceRegion plugin
```
splice_donor_5th_base_variant
splice_do…