The web VEP tool gives you a lot of useful information about your variants, but you may want more details, for example about the genes your variants overlap: maybe you want to fetch their sequences, homologues or protein domains. With a single click, you can go straight to BioMart, using your list of genes or known variants as your filter.
Continue readingCategory: Ensembl VEP
Cool stuff the Ensembl VEP can do: getting and using allele frequency data
Allele frequency data is important for variant prioritisation – it helps to identify variants that are less likely to be causing a phenotype or disease. With the Ensembl VEP, you can get allele frequencies for variants that are identical with the variants you analysed and you can use allele frequencies to filter the results of your analysis.
Continue readingCool stuff the Ensembl VEP can do: annotating SARS-CoV-2 variants
We had a number of queries about the Ensembl VEP related to its support for SARS-CoV-2. Here, we talk about how you can use the command line VEP to analyse your variants against the SARS-CoV-2 gene set from Ensembl.
Continue readingCool stuff the Ensembl VEP can do: summarise your analysis
Ensembl VEP analyses your variant alleles in detail using a flexible choice of options, but it can also create simple summary tables and graphics describing your full variant set.
Continue readingCool stuff the Ensembl VEP can do: analysis with RefSeq transcripts
By default, VEP uses the Ensembl/GENCODE transcript set when analysing your variants, but you can also choose to use NCBI’s RefSeq transcripts.
Continue readingNormalising variants to standardise Ensembl VEP output
Variants can be represented in myriad different ways; indeed, Ensembl VEP currently supports input in many different formats, including VCF, HGVS and SPDI. However, even within these specifications, variants can be described ambiguously. Insertions and deletions within repeated regions can be described at multiple different locations. For example, VCF describes variants using their most 5’ representation, while HGVS format describes a variant at its most 3’ location.
Starting in Ensembl 100, VEP optionally normalises variants within repeated regions by shifting them as far as possible in the 3’ direction before consequence calculation. This standardises VEP output for equivalent variant alleles which are described using different conventions.
Cool stuff the Ensembl VEP can do: variant citations
If you are filtering a set of variants to look for those potentially involved in disease, your first stop will probably be databases of phenotype associations, like ClinVar. There is also a lot of valuable information on variant-disease associations in the literature, which may not yet have been extracted into curated databases. It can be hard to compile lists of citations for a large set of variants, but Ensembl VEP is here to help!
Continue readingCool stuff the Ensembl VEP can do: annotating structural variants
The Ensembl VEP does not only allow you to annotate short variants, such as SNPs and short insertions or deletions, but also some types of structural variants.
Cool stuff the Ensembl VEP can do: install using Docker
We know that installing the VEP is not always trivial – there are dependencies and modules that you may or may not have already, and your existing setup may require different module versions. It’s also designed for a Linux system and installing on, for example, Windows, can be complex. To get around this, the VEP and all its dependencies are available in a Docker image, so that you can install everything with just a few simple commands.
Continue readingCool stuff the Ensembl VEP can do: write your own plugin
Plugins can be an excellent way to extend the functionality of the VEP. They can be used to look-up information in external databases or use the Ensembl API to add to or filter your VEP output. Many plugins have already been written, both by us and external groups, but with a bit of Perl you can easily write your own.
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