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: limiaoxin@mail.sysu.edu.cn
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.
IGG is free of charge. All materials on the website are provided without any warranty. Please use them at your own risk.
Fixed bugs in the function of exporting integrated genotypes
Fixed bugs in the function of integrating HapMap phased genotypes on X chromosome. Treat malesĄŻ genotypes on X chromosomes as homozygous.
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.
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.
Modify the confused pedigree input and add a hint to set maximal memory.
Optimize the usage of computational memory to handle hundreds of thousands of large SNP chips more efficiently.
1. Convert non-AB chip genotypes into the AB format genotypes.
2. Enable fast and direct downloading of HapMap phased and unphased genotypes.
1. Fasten the downloading of annotation data by a new http function
1. Allow genotypes of SNP with no strand information but non-complementary allele names to be integrated
1. Add more SNPs in the dbSNP annotation dataset
2. Export unphased reference panel genotypes for IMPUTE2
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
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.
Several minor bugs of IGG3 are fixed for Mac OS.
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.
A big update of IGG. It has a complete set of Illumina and Affymetrix gene chips; faster integration; easier useage.
Add Illumina Human Linkage-12
 Add Illumina HumanHap550-Duo and Illumina Human CNV 370-Duo
Add a summary how many markers there are per centiMorgan and per million bases
Add functions for advanced users to merge large datasets
Add a function for users to remove genotypes violating Mendelian Law
Add functions for advanced users to replace annotation files
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, ZHONGSHAN SCHOOL OF MEDICINE, SYSU, All rights reserved.