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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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We are trying to add support for multiple genomes as to start this project was only working for human GRCh38.
Work has been done at the loading step on Apr 5, 2022 to support on top of human GRCh38…
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We have a situation where possibly the pipe transformer, running VEP, is throwing data specific errors. We have no visibility into what if any errors VEP is reporting (mostly because it is running in …
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I tried to annotate my files with FunMotifs, but did not succeed:
Screenshot form the bed file:
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VEP 111 forwards requires positional arguments in the construction of the custom annotation fields which will not work with out current config and app set up.
example from their docs:
```shell
./…
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### Description of the bug
Hi, I am unable to load sentieon dnascope model using the command below.
The SENTIEONDNASCOPEMODEL points to to location of the Sentieon model
$PATH/DNAscopeIlluminaWES2.…
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Hello @apeltzer @FriederikeHanssen
This is Raghavendra,
I am currently using pyTMB.py for finding Tumor mutational burden with having VEP annotated vcf output file. But I am unable to use pyTMB.py…
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Hello, I'm trying to convert vcf file into MAF with vcf2maf, I have the environment with the packages installed, but whenever I try to convert a vcf file I got this error:
perl: warning: Falling back…
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In some scenarios, it is useful to be able not 3' shift the hgvs notations. So, it would great to be able to untoggle **shift_hgvs**.
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I'm trying to run MuPeXI pipeline with test data. There seems to be a problem with NetMHCpan, but I can't seem to fix it. I have checked the paths requested by the tool in its installation, as well as…