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Hi,
First of all, we want to thank you for this wonderful application. It has streamlined our variant annotation workflow tremendously.
We submitted the HG19 chr16-11349332-CC-TT variant to Ope…
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Hi Brent,
I am wondering how I could keep certain vcf header values after using vcfanno for example:
##SnpEffVersion and ##SnpEffCmd
After using vcfanno to merge this vcf with a VEP(ed) vcf I…
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Hi, I am trying to run VEP, but I keep getting this issue (and output file is empty):
Can't call method "seq" on an undefined value at /home/WUR/steen179/miniforge3/share/ensembl-vep-111.0-0/Bio/E…
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As a **developer** I want **to delete the step that generates a variant to gene dataset** because **it is an auxiliary concept that is only useful in the context of generating features for L2G.**
#…
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I am looking to use Varlociraptor to call SVs using candidates from several upstream callers (Delly, GRIDSS, Manta). Is there a recipe for how to configure Varlociraptor to do this?
Specifically, I…
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Hi,
I installed CADD v 1.7 and downloaded the annotations/prescored files separately and put them in the appropriate folders. I then run ./CADD.sh test/input.vcf to test the software, then I get t…
yotsa updated
1 month ago
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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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I tried to annotate my files with FunMotifs, but did not succeed:
Screenshot form the bed file:
![image](https://github.com/Ensembl/VEP_plugins/assets/73748542/2959ed7a-a052-4f76-9d28-14001abaa565)
…
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I am running the latest version (v2.2) of ScanNeo and VEP (v106.1), and successfully complete the first step. However, I got some error messages by running the second step of the workflow below:
Than…
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## Describe the issue
NC_000003.11:g.128204049_128206714del is annotated as a HIGH impact splicing variant when an explicit REF/ALT is supplied, but is annotated as a LOW impact variant w/o splicin…