What are the best tools to compare the results of the Illumina OMNI Express array and the results of the Cloninger Washington University study on the 108 schizophrenia associated genetic loci?

This is for one time use in a study with a small sample size on a tight budget so we're looking for open source or low cost tools; we have access to developers who will be providing pro bono services so we can write our own utilities or apps if necessary.

Illumina OMNI Express

https://www.genebygene.com/pages/research?goto=cma

Here is the description of the test from the web site; so far all I've been able to elicit from the company is that the results are in CSV format; I have not heard back on the availability of sample data files.

The Illumina Omni Express array is a 24-sample BeadChip belonging to the Next-Gen GWAS Omni family of microarrays designed to provide high sample throughput and comprehensive genomic content. It includes a total of 730,525 genome-wide markers with an average spacing of 4kb and targets a minor allele frequency of 5% as reported in the HapMap data.

News story: https://news.wustl.edu/news/Pages/27358.aspx

More detailed technical results: http://www.nature.com/nature/journal/v511/n7510/full/nature13595.html

Biological insights from 108 schizophrenia-associated genetic loci

Below is an example of the format of the study results:

indexSNP codingVariant R2 gene change CHR BP A1A2
rs56873913 rs2288920 0.761755 PRRG2 G116C 19 50091199 TG
rs6670165 rs3176443 0.900709 FAM5B L390V 1 177280121 TC

UPDATE - received sample data from the company:

[Header]
GSGT Version    1.9.4
Processing Date    8/12/2014 13:29
Content        humanomniexpress-24v1-0_a.bpm
Num SNPs    716503
Total SNPs    716503
Num Samples    1
Total Samples    574
[Data]
Sample ID    Chr    Position    Log R Ratio    SNP Name    B Allele Freq    GC Score    Allele1 - Plus    Allele2 - Plus
GRCXXXXXXX    12    126890980    0.0865    rs1000000    0.9957    0.7839    G    G
GRCXXXXXXX    3    183635768    0.0412    rs1000002    0.4811    0.8832    T    C
GRCXXXXXXX    4    95733906    0.0795    rs10000023    0.5026    0.8188    T    G