Illumina SNP Input Engine

The Illumina SNP Input Engine imports genotype data from files generated by Illumina®’s BeadStudio software into a SAS data set that can be used as input for the advanced JMP Genomics analytical processes.

What do I need?

The Illumina SNP Input Engine can import data from either:

•	the Full Data Table produced by the BeadStudio Genotyping Module, or

•	the Final Report file generated by the BeadStudio Report Wizard.

The Full Data Table presents data in the tall format, having SNPs represented in rows and individual samples presented in columns. Genotype data are represented by characters, with AA and BB indicating different homozygotes. Heterozygotes are indicated by AB. Only genotype data is imported from this file. Additional information about the individual samples, the SNPs and chromosomal position, is imported from the sample and map files.

The Final Report file presents the data in a stacked format; each combination of SNP and individual is presented in a separate row. The format of the genotype data, which can vary depending on format specified by the BeadStudio Report Wizard, must be known.

The following example uses a proprietary data set provided by Illumina. These files, which include the Human1_118dna_109365snps_FinalReport.txt final report file, the Samples Table.txt sample file, and the SNP_Map.txt SNP map file, were saved to a new Illumina folder created in the JMP Genomics Sample Data folder.

For detailed information about the files and data sets used or created by JMP Life Sciences software, see Files and Data Sets.

Output/Results

The output data sets generated by this process are listed in a Results window. Refer to the Illumina SNP Input Engine output documentation for detailed descriptions.