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We have downloaded loftee plugin from grch38 branch and tried to use it but encountered the below error. Could you please have a look and assist ?
WARNING: Failed to compile plugin LoF: Attempt to …
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My command is
```
SURVIVOR merge vcfs.txt 0.1 0 1 0 0 100 svim-asm_variants.vcf
```
Below are some lines of the SURVIVOR output which I changed format using bcftools. I wonder if I can treat the …
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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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When converting c. HGVS from cDNA to genome coordinates, VEP appears to not take into account alignment gaps, where the cDNA has insertions/deletions vs the reference sequence.
Submission example:
…
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Hi,
I'm struggling to set LoF plugin in my VEP. After installing LoF.pm and related files addressed in [here](https://github.com/konradjk/loftee), I ran vep using script below:
`vep98=/data/softwa…
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Hi,
I am trying to run MuPeXi on the given example VCF (https://raw.githubusercontent.com/ambj/MuPeXI/master/data/example.vcf) using the below command but end up with error:
`MuPeXI.py -v data/e…
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See
https://github.com/bigdatagenomics/bdg-formats/issues/202
https://github.com/heuermh/bdg-formats/blob/docs/docs/source/transcript-effects.md
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Caching VEP annotations (instead of re-running VEP on all variants each time) would speed up the ClinVar pipeline. This would be nice for updating ClinVar data more frequently.
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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…