Golden Helix, SNP and variation Suite is mainly targeted for SNP, CNV , GWAS analysis. The latest version provides NGS analysis tools. Its modular design enables the facilitation of usability upgrades.
This software has a unique approach that enables the direct comparison of GWAS and sequencing results.
According to them "Considering that the cost of sequencing may still be cost-prohibitive on a large scale, one unique approach is to combine next-generation sequencing with the latest custom microarray technologies to maximize your GWAS results. By sequencing a modest number of cases, you can use SVS to identify an enriched panel of variants that are "common" in cases, though rarer in the general population. You can then design a more affordable custom microarray panel based on these variants and run them on all samples in typical GWAS fashion."