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

9 things you didn’t know about bioinformatics

Lessons. Today was the first day of our bioinformatics workshop in Leuven, Belgium. We started out with some basic command line programming and eventually moved on to working with R Studio. What is this all about? It’s about getting some basic understanding of what your computer does and how your computer handles files. It’s about good data and bad data and losing the fear of the command line. We collected responses from the participants today about today’s take home messages. Continue reading

Axiomatic – identifying a novel epilepsy gene that was hidden right before your eyes

The Hague, winter of 1997. Last week challenged my most basic beliefs, which reminded me of “Axiomatic”, a collection of science fiction short stories by Greg Egan. While on holiday in the Netherlands in 1997, I had bought this book in the Den Haag Centraal bookstore, and subsequently lost it or gave it away. I only remembered the title three weeks ago, and ordered it online. The book arrived at the same time that news from Antwerp twisted my brain. In the signature story of “Axiomatic” with the same title, a man acquires a nano-robot based implant that allows him to change his innermost convictions (I told you that it’s science fiction, right?). He basically wants to have the courage to kill the man who murdered his wife. After carrying out his revenge and after the effect of the axiomatic implant has worn off, he starts craving for more, since he is missing the certainty in his life that the implant had given him. I needed to adjust my deeply held expectation on how to find de novo mutations after Tania, a PhD student in the Antwerp lab, had pulled out a de novo mutation in one of our trios that Denovogear had missed. This mutation turned out to be another hit in a gene that we had seen before. Continue reading

How to detect de novo mutations in exome data

Taking things apart. Looking for de novo variants using trio exome sequencing is a powerful technique to identify disease-related genes. After having introduced samtools during the last post, this will be post 2/3 in a series on how to perform an analysis of exome data for de novo variants. This time, I would like to take apart the methods that take us from Gigabyte BAM files to small tables with likely variants. So buckle up. Continue reading

Exploring samtools – Green Eggs and Ham (*.bam)

That Sam I Am.  The entire field of high-throughput genomics appears to be inspired by the American children’s book author Dr. Seuss. Given that we are currently reading through the original books almost on a daily basis due to the presence of a toddler in our home, mentioning *.sam files, *.bam files or sam2bam routines always makes me smile. However, this is not a post about children’s books; it’s about a likely 2013 trend in genomic research, the redefinition of the boundary between genome center and end user and the laptopification of life sciences. Continue reading