Downloading GenGen

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

GenGen main package

The GenGen main package can be downloaded below (2010Apr29 version). Users pointed a few bugs in the old program but I have been slow in updating website even though I fixed these issues a while ago. The main package DOES NOT include the necessary library files. The executable for Windows depends on Perl 5.8.8 32bit, so for any other Windows architecture, users need to compile source code.

• gengen.tar.gz

Additional update 2010Jun24: A few people asked me the best way to identify SNPs in a particular array (for example, Illumina array with 550K markers), that are best proxy for a list of candidate SNPs (for example, dozens of SNPs reported in a meta-analysis paper using imputation data). The find_ld_snp.pl program is designed to do this: just run "find_ld_snp.pl snplist.candidate snplist.550karray hapmap_CEU_r23a" and it will tell what are the best SNPs to use in the Illumina array, their r2 measures, and their distance to each other. Use the "-m" argument to read the manual first.

UPDATE 2014Aug13: An updated convert_bim_allele.pl is available here. Additional "forward" keyword is added. Note that 'dbsnp' is not equal to 'forward', since some dbSNP records are in reverse strand.

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).

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

Contact me with issues/bugs in these files as they were not tested by me.

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.

• 2010Apr29: fixed multiple bugs, including issues with permutation procedure in QT analysis, issues with BIM conversion for cnv markers.
• 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.