GenGen main package
The stable version of GenGen main package can be downloaded below. The main package DOES NOT include the necessary library files.
Supplementary library files
SNP-gene mapping files for various Illumina and Affymetrix SNP arrays, as well as SNPTable file for commonly used arrays, can be downloaded below.
Among the SNP-gene mapping files, hh550* are for HumanHap550 array, hhall* are for other Illumina Infinium arrays, affy500k* are for Affymetrix 500K arrays, gw6* are for Affymetrix genome-wide 6.0 arrays. You can contact me directly to get SNP-gene mapping annotation for other arrays. Or, you can follow the instructions to generate a custom annotation file using the scan_region.pl program included in the package. Among the SNPTable files, hh550_610.snptable is for Illumina 550K or 610K arrays (all versions), and hh1mv13.snptable is for Illumina 1M arrays (version 1 or 3).
SNPTable file for Illumina arrays and Affymetrix arrays
- CNV370 version 1 array
- CNV370 version 3 array
- Cyto12 version 1 array
- HumanHap1M version 1 array
- HumanHap1M version 3 array
- HumanHap550 version 3 array
- Human610 version 1 array
- Human660 array
- Omni version 1 array
- Omni Express version 1 array
Contact me with issues/bugs in these files as they were not tested by me.
You can generate a SNPTable file yourself by downloading the manifest file from Illumina. This is a comma-delimited CSV file and you only need to extract the four relevant columns from this file, then save as tab-delimited formats.