Downloading GenGen

GenGen is a suite of free software tools to facilitate the analysis of high-throughput genomics data sets.

GenGen main package

A patch (2009Sep21) for the convert_bim_allele.pl file is provided here (right click mouse and select "save as..."). It fixed an issue when converting dbsnp->top format, and added two arguments controlling the handling of zero alleles and mismatched alleles.

The GenGen main package can be downloaded below (2009Aug30 version). The main package DOES NOT include the necessary library files. Please also download the library files below (the main package will be updated in a different pace as the supplementary library files in the future).

• gengen.tar.gz

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.

• gengenlib.tar.gz

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).

Archives of older versions of GenGen

The older versions of GenGen are no longer archived, and it is recommended to use only the latest version.

• 2009Aug30: reorganize the directory structure and minor fixes to improve compatibility with various system architecture. Executables for Windows (cygwin and MS Windows) included.
• 2009Aug07: Added a few programs for helping with genotype imputation and allele coding conversion. Fix the bugs in calculate_association.pl: (1) the --allmarker argument does not work as expected, (2) alleles that were labeled as 3 or 4 are not recognized correctly, (3) the "NA" cannot be recognized correctly in phenotype file for QT analysis.
• 2009Jan05: Changes in chrX association test.
• 2008Oct04: Several function enhancements: calculate_association.pl now handle PLINK files (TFAM/TPED) directly; calculate_gsea.pl handle --pvalue_flag by a differnt formula; updated BioCarta/KEGG/GO pathway definition.
• 2008May19: Several function enhancements for various prorams. Renamed TDT.pm to GWA.pm. Better handling of different computer architecture/platform.
• 2008Jan14: Several function enhancements for various prorams. Fix allele frequency bug in output of calculate_association.pl.
• 2007Dec13: added more programs in the public release.