I have done part of the bioinformatics analysis of my Illumina HiSeq DNA-seq data, all of them were filtered, aligned and SNPs were called out. I'm using AVADIS NGS software to do all the analysis. Now I get a lot of output data(all the SNPs) from my different 3 groups of subject. Any idea on what kind of downstream analysis I can do to compare within these 3 groups? I get quite a number of known and novel SNPs from all these 3 groups. A bit confusing on what to do next as I'm still new in this.