IGG 3.0 – Integrate Genotypes for genome-wide Genetic studies

IGG 3.0

:: DESCRIPTION

IGG (Integrate Genotypes for genome-wide Genetic studies) is an open-source Java package with graphic interface to efficiently and consistently integrate genotypes across high throughput genotyping platforms (e.g., Affymetrix and Illumina), the HapMap genotype repository (http://www.hapmap.org/), and even genotypes from the collaborators’ projects. It is equipped with a series of functions to control qualities of genotype integration and to flexibly export genotypes for genetic studies as well.

::DEVELOPER

Miao-xin Li ,The University of Hong Kong

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 IGG

:: MORE INFORMATION

Citation

Li et al. (2009)
IGG3: a tool to rapidly integrate large genotype datasets for whole-genome imputation and individual-level meta-analysis.
Bioinformatics 25(11):1449-50.

META 1.6 – Carryout Meta-analysis of Genetic Studies

META 1.6

:: DESCRIPTION

META is a program for the meta analysis of genome-wide association studies. The program is designed to synthesizing the evidence from different association studies. Particularly, the program is able to work seamlessly with the output of SNPTEST [1] . This program was used in the meta analysis of the genome-wide association studies of smoking.

::DEVELOPER

Zhan SuJonathan Marchini

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 META

:: MORE INFORMATION

Citation

J. Z. Liu, et al (2010)
Meta-analysis and imputation refines the association of 15q25 with smoling quantity.
Nature Genetics, 42, 436-440

GeneLink 1.7 – Data Management System to Facilitate Genetic Studies of Complex Traits

GeneLink 1.7

:: DESCRIPTION

GeneLink is a data management system designed to facilitate genetic studies of complex traits.In contrast to gene-mapping studies of simple Mendelian disorders, genetic analyses of complex traits are far more challenging, and high quality data-management systems are often critical to the success of these projects. For this reason, we have developed GeneLink, a Web-accessible, password-protected Sybase database that enables genotypic data to be merged easily with pedigree and extensive phenotypic data. GeneLink was designed specifically to facilitate large-scale (multi-center), genetic linkage or association studies and is a powerful tool for complex trait mapping. GeneLink securely and efficiently handles large amounts of data, as well as provides additional features to facilitate quality control and analysis of data generated. In particular, chromosome-specific data files containing marker data in genetic map order can be downloaded in various formats appropriate for downstream analyses (e.g. GAS, LINKAGE). Furthermore, an unlimited number of phenotypes (either qualitative or quantitative) can be stored and analyzed. Finally, GeneLink generates several quality assurance reports, including genotyping success rates of specified DNA samples or success and heterozygosity rates for specified markers. GeneLink has already proven an invaluable tool for complex trait mapping studies and is discussed primarily in the context of our large, multi-center study of hereditary prostate cancer (HPC).

:DEVELOPER

NHGRI

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Unix
  • Sybase SQL
  • Perl
  • Apache

:: DOWNLOAD

  GeneLink

:: MORE INFORMATION

Citation:

Gillanders, E.M., Masiello, A., Gildea, D., Umayam, L., Duggal, P., Klein, A., Jones, M., Freas-Lutz, D., Ibay, G., Trout, K., Wolfsberg, T.G., Trent, J.M., Bailey-Wilson, J.E., Baxevanis, A.D. 2004.
GeneLink: A Database to Facilitate Genetic Studies of Complex Traits.
BMC Genomics 5(1):81.