inPHAP: Interactive visualization of genotype and phased haplotype data

To understand individual genomes it is necessary to look at the variations that lead to changes in phenotype and possibly to disease. However, genotype information alone is often not sufficient and additional knowledge regarding the phase of the variation is needed to make correct interpretations. Interactive visualizations, that allow the user to explore the data in various ways, can be of great assistance in the process of making well informed decisions. But, currently there is a lack for visualizations that are able to deal with phased genotype data. inPHAP is an interactive visualization tool for genotype and phased haplotype data. It features a variety of interaction possibilities such as zooming, sorting, filtering and aggregation of rows in order to explore patterns hidden in large genetic data sets. Due to its highly scalable design, inPHAP can be applied to datasets with up to 100 GB of data. As a proof of concept, we apply inPHAP to the phased haplotype data set of Phase 1 of the 1000 Genomes Project and demonstrate its ability to show genetic variations both, on the population as well as on the individuals level. As of today, inPHAP is the only visual analytical tool that allows the user to explore unphased and phased haplotype data interactively. It closes the gap between common visualization tools for unphased genotype data and introduces several new features, such as the visualization of phased data. inPHAP is available for download at http://bit.ly/1iJgKmX.