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Apparently something changed in VEP, and now the `-u` flag passed by bcbio isn't actually honored anymore. That means that the installer looks for the tarball in `/tmp` rather than the path bcbio give…
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It seems that recent (VEP108+) of VEP have broken compatibility with the way we parse and pass vep parameters in vep_gatk.
In summary, cache version must be set with --cache_version and --cache mu…
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/* --- PROJECT - VARIANT PREDICTION IN CYP2D6--- */
Investigate CYP2D6 Pharmacogenetic Variation:
- Involved in metabolism of nearly 25% of clinically prescribed medications
- Highly polymorphi…
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Hi,
I am able to run 30 samples with no errors. However, about 5 additional samples get stalled, meaning VEP is running indefinitely with no error.
It turns out that all 5 samples have large RE…
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Hi everyone
I want to run vcf2maf to convert vcf to maf but i have some problems to install dependencies in perl.
**[vcf2maf](https://github.com/mskcc/vcf2maf)** need [VEP](https://github.com/E…
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## Describe the issue
When you run VEP against a VCF record with a reference that is different from the fasta sequence, the consequences are calculated against provided base, while HGVS is calcualt…
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See here: https://github.com/mskcc/vcf2maf/issues/95
Currently if using hg19 ref fasta, it complains for the VEP cache vs fasta discrepancy
![image](https://user-images.githubusercontent.com/381…
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Hello,
I'm getting the following errors that result in a downstream termination of the pipeline.
```
Error in rule get_genome:
jobid: 4
output: resources/genome.fasta
log: logs/…
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https://github.com/bm2-lab/pTuneos/blob/e6cfd0e1b57bf04fe60baee40efe4f3b0c8d56f3/src/core/VariantCallingFormat/VCFprocessor.py#L72
For INDELs, it seems that no Consequence is missense_variant ?
pl618 updated
4 years ago
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Here is a very rough first cut at an alignment authoring api. I obviously need to learn a lot about python so forgive the non-standard function signatures.
I think the goal is: Keep it simple - dev…