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When I was running ScanNeo2, several samples encountered errors during the VEP annotation process, specifically for the main task of SNVs. The following error occurred for all of them.
localrule ann…
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Hi team,
I annotated my variants using vep with spliceAI plugin. The output file contains all the multiple columns along with SpliceAI_pred column.
But the values in the column for a variant, for …
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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 issue
vep give different result when using multi-thread(--fork).
problem:
Some gene(like ENSG00000169047 or ENSG00000168769) will loss its refseq HGNC ID(near field EntrezGene) wh…
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Hi, it would be really helpful if VEP annotations could be included or if you had any good ideas on how to cross reference. Currently I'm having to generate vcfs for the positions I'm interested in an…
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## Describe the issue
I encountered the same problem as shown in the figure when using the DownStream plugin (there is no such problem when using --hgvs). Following these three instructions, I update…
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Hello there,
My file was annotated using VEP, and I am trying to convert the annotated VEP output to a format accepted by VPOT.py using these commands:
python3 ../VPOT_6_1_convertVEP.py utility …
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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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**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 …