I’m always interested in new strategies to visualize data. So when I saw discussion about a tool to help analyze family genomic data, I went to have a look. TrioVis is a new software tool that offers nice visualization and filtering strategies for exploring parent and child trio data sets. These data sets will become increasingly common as families seek out information for uncharacterized medical situations that may be affecting their kids. But they are being widely used already in many research situations.
TrioVis relies on the common VCF or Variant Call Format files that are generated from sequencing data. You can have a look at the types of information they carry at the 1000 Genomes project site. These files are created for each parent and the child in a trio situation, and then they are visualized with TrioVis in this manner:
The user interface consists of five sections: the main table (Fig. 1A), the global variant count bar graphs (Fig. 1B), the variant frequency sliders (Fig. 1C), the coverage sliders (Fig. 1D) and the histogram view (Fig. 1E). Each section focuses on a specific aspect of trio data and offers specific interactive features to calibrate the thresholds. Father, mother and child are colour-coded in green, orange and blue, respectively.
You can read the paper for more details on their goals and strategies. They also point to some 1000 Genomes project sample data you can use to run their tool.
But I also want to commend the TrioVis folks for putting a screencast of their tool right in their abstract. So their video is what I’d like you to view as this week’s Tip of the Week:
Right now there isn’t a web interface to use, but I noticed in their paper that they plan to integrate this into Galaxy. I think that’s another great idea on their part.
So if you find yourself exploring family trio data sets, consider a look at TrioVis.
Hat tip to Justin Johnson for drawing my attention to this paper and resource.
— Justin H. Johnson (@BioInfo) May 16, 2013
TrioVis software: https://bitbucket.org/biovizleuven/triovis/wiki/Home
TrioVis video: http://vimeo.com/user6757771/triovis
Sakai, R., Sifrim, A., Vande Moere, A., & Aerts, J. (2013). TrioVis: a visualization approach for filtering genomic variants of parent-child trios Bioinformatics DOI: 10.1093/bioinformatics/btt267