IGG: A tool to Integrate Genotypes for genome-wide Genetic Studies
 
 
The current version IGG is v3.0 . If you have any question about IGG, please email: limx54@yahoo.com
Type File Version
Linux (i686) IGG3.tar.gz v3.0
MS Windows IGG3.zip v3.0
Apple Mac (PPC) IGG3.zip v3.0
User Manual User Manual3.pdf v3.0
Java Source Codes IGG3.src.tar.gz v3.0
Hint: Example inputs have already been included in a folder "inputSamples" of the downloaded. Or a set of example inputs can be generated by Tools->Generate Sample on the the main menu.
Disclaimer:
IGG is free of charge. All materials on the website are provided without any warranty. Please use them at your own risk.
Updated:
18/12/2011
Fixed bugs in the function of exporting integrated genotypes
26/02/2011
Fixed bugs in the function of integrating HapMap phased genotypes on X chromosome. Treat malesĄŻ genotypes on X chromosomes as homozygous.
28/10/2010
1. Recognize HapMap data with various reference genome coordinates: Build 35, 36 and 37.
2. Export data for imputation with various reference genome coordinates: Build 35, 36 and 37.
18/06/2010
Support the Plink binary PED format(http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml#bed). Input and output the *.bed, *.fam, and *.bim files.
14/04/2010
Modify the confused pedigree input and add a hint to set maximal memory.
20/11/2009
Optimize the usage of computational memory to handle hundreds of thousands of large SNP chips more efficiently.
19/10/2009
1. Convert non-AB chip genotypes into the AB format genotypes.
2. Enable fast and direct downloading of HapMap phased and unphased genotypes.
06/09/2009
1. Fasten the downloading of annotation data by a new http function
05/07/2009
1. Allow genotypes of SNP with no strand information but non-complementary allele names to be integrated
20/06/2009
1. Add more SNPs in the dbSNP annotation dataset
2. Export unphased reference panel genotypes for IMPUTE2
11/05/2009
1. Update the Affymetrix annotation to be na28
2. Add a function to check the latest version of IGG
3. Add a function to summarize the SNPs unexpected allele names
23/03/2009
1. A new input format for general genotype datasets with known strand formation has been added, which flexibly covers many popular formats supported by genetic tools including the linkage package and Plink.
2. A new export format for BIMBAM (http://quartus.uchicago.edu/~yguan/bimbam/index.html) has been added.
07/02/2009
Several minor bugs of IGG3 are fixed for Mac OS.
01/01/2009
IGG3 beta is released. It has the following features.
1. Very fast integration of whole-genome genotypes for poplular Affymetrix and Illumina DNA chips;
2. Ability to integrate whole-genome genotypes of tens of thousand subjects;
3. Integration of PHASED and unphased HapMap genotypes of Phase I+II+III;
4. Specical functional module to ease genotype impuation.
07/09/2008
A big update of IGG. It has a complete set of Illumina and Affymetrix gene chips; faster integration; easier useage.
30/06/2008
Add Illumina Human Linkage-12
24/04/2008
 Add Illumina HumanHap550-Duo and Illumina Human CNV 370-Duo
18/02/2008
Add a summary how many markers there are per centiMorgan and per million bases
08/1/2007
Add functions for advanced users to merge large datasets
07/12/2007
Add a function for users to remove genotypes violating Mendelian Law
05/16/2007
Add functions for advanced users to replace annotation files
Archive:
Type File
Linux (i686) IGG.tar.gz
MS Windows IGG.zip
Apple Mac (PPC) IGG.zip
User Manual User Manual2.pdf
Java Source Codes Upcoming
 
Linux (i686) IGG.tar.gz
MS Windows IGG.zip
Apple Mac (PPC) IGG.zip
User Manual User Manual.pdf
Java Source Codes IGG.src.tar.gz

Miao-xin Li, Department of Biochemistry, The University of Hong Kong, All rights reserved.