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 readingAuthor: Astrid (Outreach)
Cool 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 readingEnsembl under lockdown – Part 4
Whilst the UK has started to lift some of the COVID-19 lockdown restrictions, Ensembl staff are still working from home. We are fortunate that we can continue to do this and that there are flexible working arrangements in place to support us.
Continue readingEnsembl under lockdown – Part 3
The start of the lockdown due to the COVID-19 pandemic and the changes it brought has affected all of us in different ways. In this blog, we hear from Michal and Beth.
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.
Ensembl under lockdown – Part 2
It’s now ten weeks since we have started working remotely because of the COVID-19 pandemic. The novelty of the situation is gone and we got accustomed to the ‘new normal’.
Continue readingEnsembl launches COVID-19 resource
Today, Ensembl has joined the international scientific effort to tackle the COVID-19 pandemic. COVID-19 is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has spread rapidly since emerging in late 2019. Our SARS-CoV-2 genome browser and related resources at covid-19.ensembl.org are intended to support both basic research and ongoing work to develop treatments, diagnostics and vaccines.
Continue readingEnsembl under lockdown – Part 1
Ensembl staff have been working from home due to the COVID-19 pandemic for eight weeks now. We transitioned to remote work from 16 March – two days before the closure of EMBL-EBI and a week before the Prime Minister announced the UK lockdown on 23 March.