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Hi!
Our analysis and the design of Scout, for historical reasons, heavily rely on CADD. However, there are now several new in silico prediction tools available. The advantage of CADD is that …
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**Describe the solution you'd like**
VEP all reference data. Roadmap deliverable.
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First of all thanks that more and more packages are available for arm64. `ensembl-vep` is available as `noarch`. However, it cannot be installed since neither `perl` nor `perl-bio-db-hts` is availble …
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This ticket will include scoping iterations for the VEP widget on the variant page.
Please note that at time of issue opening, the variant index data/API is not completed e.g. the data team is work…
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Dear Developers,
I have my vcf file generated using UCSC HG38. I realized that is a zero-based coordinate system.
I annotated the vcf with VEP and I also got to know that Ensemble uses a [one-based …
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Annotate NMD-triggering/skipping nonsense variants through the VEP plugin:
http://www.ensembl.org/info/docs/tools/vep/script/vep_plugins.html#nmd
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### Description of the bug
- querynator uses the gnmoAD allele frequency, annotated by `VEP`
- VEP annotates the gnomAD AF based on their genomic data or exonic only
- VEP names the fields `gnomADg…
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### Description of the bug
This bug has been around for a while now. When Sarek encounters an error is will often issue the correct error message along with a couple of wrong error messages. The wron…
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I installed VEP through
`conda install -c bioconda ensembl-vep` .
And my command for vcf2maf is
`perl vcf2maf.pl --input-vcf 915.raw.somatic.vcf --output-maf 915.raw.somatic.maf --ref-fasta /st…
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Hi,
When I running this command :
`vcf2maf=/data/jiaf/wes_cancer/biosoft/vcf2maf/vcf2maf.pl
vep_path=~/miniconda3/envs/vep/bin/
GENOME=/data/jiaf/wes_cancer/biosoft/gsutil/gatk/hg19/v0/Homo_sapie…