SNPs analysis - (Jul/01/2014 )

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. 

Many thanks. 

You could either organize them into groups or just analyze them separately. Feed your results into SeattleSeq and it will return you a spreadsheet that gives the standard dbSNP information. From there, you can compare the frequencies within the population and determine which SNPs are novel