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

The Excel contagion

The tale of 16,000 genes. For a recent analysis, I wanted to compile all the gene names of variants that were found in 12 of our EuroEPINOMICS research patients. Since I was planning to do some statistical analysis as well, I used the R package for this, my personal favourite for all kinds of statistics. I also have  weak spot for Minitab and never got along with SPSS, but that is a different story. After I filtered and sorted the genes alphabetically, the following picture made me smile and gave me a reason to write a bit about role of Microsoft Excel for exome analysis…

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