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Should be just a matter of changing `lapply` to `.runFunctionInParallel` in `generateCandidates` function. Will probably have to change filenames in `.getVariantsForRange` as well.
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**Snakemake version**
### `Snakemake`
> 5.23.0
### Wrapper
**Issue**
I'm trying to adapt my regular VEP code to use the snakemake wrapper instead but am running into an issue.
I …
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For each VEP gene hit, collect the associated GO terms and generate a table with the fields cultivar, snp, gene, go terms, and any other interesting annotations from VEP.
Could use the GO VEP plugi…
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### Description of the bug
Hi there
Thank you for the pipeline, it was working good using just frebayes. now add sarek and mutec.
I need to find structural mutations, and de novo mutation, however …
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I think that it would be feasible to run the VEP-compatible releases in CI.
The main limitation will be memory usage. A possible workaround may be using something like [orjson](https://github.com/i…
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Should `ecl_FK4` be deprecated?
Its description starts with "old", as for the other deprecated terms.
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Hi,
I have noticed a couple of issues with excessive warnings when loading extra VEP columns in GEMINI 0.16.3. I see that the routine calls the annotate tool to load extra VEP columns. This would be …
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A CCB researcher emailed about how 17:7574012 G>A has HGVS of ENST00000269305.4:c.1015G>T
As it's -'ve strand you'd think given the ref G would be complement C ie HGVS should be ENST00000269305.4:c.…
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Dear open-cravat team,
Please add, **[GeneBe](https://genebe.net/)** plugin (ACMG score and classification) in **open-cravat**. VEP and MobiDetails added this plugin in their pipeline/analysis.
…
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Hi,
I started using the tool to calculate TMB by whole exome sequencing. Thanks for developing it!
As I usually annotate my VCFs with Ensembl VEP, I tried to create a configuration file for annotat…