Exomes on the go – adventures with wANNOVAR

Going cloud. This post is about my most recent discovery when I was trying to modernize some of the bioinformatics tools that I had on my laptop. My experience with variant annotation is a good example of the latest trend in bioinformatics: replacing precise, but difficult-to-use tools by web-based convenience – I didn’t need to install anything after all. This is a brief journey into the world of variant annotation, taking advantage of my new favorite tool, wANNOVAR and applying it to the Epi4K dataset. Continue reading

The day I fell in love with Varbank

De novo. Three months ago, I performed a trio exome de novo analysis in a patient-parent trio. From my iPad, in a hotel room in Paris. When I got home a few days later, I was excited to tell my students that the analysis worked. They looked at me slightly confused: “What’s the big deal? We had the analysis complete already a week or so ago.” Last year at this time, I was proud that our lab had established a fully functional de novo analysis pipeline. Suddenly, it’s not a big deal anymore. What happened? Let me tell you about Varbank. Continue reading

A look back at the Leuven NGS bioinformatics meeting

Program completed. On Sunday, we finished our EuroEPINOMICS next generation sequencing (NGS) bioinformatics meeting. After working through the command line, running scripts, and staring at black screens with white cursors, we completed our four day course by looking at the more user friendly, web-based tools that the NGS world has to offer, including Galaxy, Varbank, and Ingenuity. I think it was the general consensus among the participants that this was the bioinformatics meeting that we needed in order to understand the data that we generate and deal with on day-to-day basis. These were my favorite sound bites of our meeting. Continue reading