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Here is a description of the intensity files

1) The raw intensity files is a direct export of the raw intensity file from the Illumina IDAT files
2) The normalized intensity file is generated by normalizing the raw intensity file using the Illumina normalization algorithm (as implemented in Bead/GenomeStudio) and 
then scaling those values by a factor of 2000 in order to make the data range favorable for Birdsuite
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Here is a description of the processing used for the VCF and the annotations of the VCF file:

Omni genotypes were called using GenomeStudio v2010.3 with the calling algorithm/genotyping module version 1.8.4 using the default cluster file 
HumanOmni2.5-4v1-Multi_B.egt.  The data were exported from GenomeStudio and converted to a VCF using a custom script - The human_b36 data set was used for mapping 
reference allele.  The VCF was subsequently lifted over to HG19 (using human_g1k_v37 data set).

The b37 set is now found in the phase1 analysis results directory together with phaseed haplotypes for these sites

ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/omni_haplotypes/

The following filters were applied to the VCFs:
ID=badAssayMapping,Description="The mapping information for the SNP assay is internally in consistent in the chip metadata"
ID=dup,Description="Duplicate assay at same position with worse Gentrain Score"
(There are duplicate SNPs on the chip - they use different assays and we use a filter to exclude the non-preferred)
ID=refN,Description="Reference base is N. Assay is designed for 2 alt alleles
ID=NOT_POLY_IN_1000G,
Description="Alternate allele count = 0
(No samples were found in the 1000G data set that had calls on the alternate allele)
ID=id5,Description="Within 5 bp of an known indel
ID=id10,Description="Within 10 bp of an known indel
ID=id20,Description="Within 20 bp of an known indel"
ID=id50,Description="Within 50 bp of an known indel"
(indels were mapped using the file "1kg.pilot_release.merged.indels.sites.b36.vcf" kindly provided by Mark DePristo)