####Display genome-wide variant calls using a hilbert-curve representation.
To find out the meaning of the different colours, check out the legend.
####What does it do exactly? So far this repository contains code to produce a hilbert curve based representation of genomic variants identified by GATK. First the GATK output needs to be parsed (parseVCF.sh) to put the variant information in a format needed for the visualization code (GenomeViz.R). So far GENE_NAME cannot be included but this is a TODO. The visualizing code (GenomeViz.R) assumes that about 4 Million high quality (PASS) variants are reported in the VCF file. If significantly more or less variants are reported the hilbert curve level (standard is 11) needs to be increased (to 12) or decreased (to 10) in the code (GenomeViz.R). At a certain point a list of variants will be displayed and the user will be asked to select one of them as "focus variant". This focus variant will then be displayed in the last frame.
The output is a series of .png files plotting the variants in hilbert representation in different zoom stages (corresponding to hilbert levels 0-11). Each zoom stage is represented with and without focus rectangle. Additionally the legend explaining the color code and stating the number of variants in each category is plotted in Sample_legend.png.
The .png files can be loaded in an animated gif maker (e.g. http://sourceforge.net/projects/gifapp/) and put together as an animated gif. 1 second per frame has been found to be a good speed.