Some Variant Effect Predictor (VEP) jobs are small, just ten or fewer variants, and that’s easy. Some VEP jobs are big, if you do variant calling on one whole human genome, that’s five million variants! The more variants you have, the more computing power the VEP needs to process them, which can make it slow. But there are ways to speed it up.
Author: Emily (Outreach)
Cool stuff the Ensembl VEP can do: Filtering
The VEP (Variant Effect Predictor) is our most popular tool and is incredibly useful for annotating genetic variants with the genes they hit and what effect they have on them. But did you know you can filter your results? Both in the web interface and using the script?
Do you use transcripts for your work?
Ensembl and NCBI have been working to align the GENCODE and RefSeq reference transcripts. As part of that effort, we are also developing plans to define a primary transcript for every gene as well as a minimal set of clinically relevant transcripts. To guide that effort, we have developed a small survey to get input on how to define the primary transcript and whether this would be important to your work.
The survey should only take 10 minutes or less and you will have the opportunity to sign up for follow-up info about this project if you are interested.
2018 – a year of conferences
We think conferences are great opportunities to use talks and posters to tell people about all the cool stuff we’re developing, provide training with workshops and learn more about what’s going on in our fields of interest. Ensembl team members attend many conferences a year and 2018 is no exception, we’re planning to attend twenty (so far)!
Getting to know us – Carla from Compara
This month we’re meeting Carla from our comparative genomics team (which we call compara).
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Learn to use the Ensembl Perl API
We’re holding an Ensembl Perl API course at the Genome Campus in the UK in April. The course give you chance to learn how to access the database directly from the people who produce the databases and write the APIs themselves. It is aimed at bioinformaticians and wet-lab scientists who are familiar with Object Oriented Perl.
This four-day course costs only £140, which includes daily transport to the campus from Cambridge city centre and refreshments (the fee is to cover only these expenses).
Please visit the course page for more details on the content and how to apply.
Getting to know us: Thomas from Regulation
This December, we’re meeting Thomas Juettemann, who is part of our Regulation team.Continue reading
Tell us what you think
We’re always looking to improve Ensembl to make your research easier. To do this, we’re looking to find out more about you, how you use Ensembl and what you find useful or would like to see improved. The survey should take no more than 10 min. If you’d like to help make Ensembl better, please click on the link below:
Ensembl Genomes 37 is now live
We’re pleased to announce the latest release from Ensembl Genomes. There’s new data and software available. Find out more:
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Getting to know us: Sophie from the Research Management Office
Our latest introduction to the Ensembl Team post comes from Sophie Janacek, who takes care of all our money.