IMPUTE and other GWA tools

Description

IMPUTE is a tool for genotype imputation in genome-wide association studies and fine-mapping studies based on a dense set of marker data (such as HapMap). Other genome-wide association tools available in the same package include:

CHIAMO - a genotype calling algorithm for multi-cohort studies
GTOOL - a program for (a) generating subsets of genotype data, and (b) converting genotype data between the PED file format and the FILE FORMAT used by SNPTEST and IMPUTE.
SNPTEST - a program for Frequentist and Bayesian tests of SNP association with binary (case-control) and quantitative phenotypes that takes genotype uncertainty into account
HAPGEN - a program to simulate case control datasets at linked SNP markers conditional upon a set of known haplotypes

Availability

Installed on the cluster.

More information

Although BMI doesn't directly support this software, we encourage its use and will try to answer questions should they arise. Simply send email to the BMI Help Desk

Need Help?

For technical assistance with other research software, email software@bmi.cchmc.org. For basic desktop support or assistance with clinical information systems, call the Cincinnati Children's Service Desk, 513-636-4100, or visit the Information Services CenterLink site. UC employees should call the UCit Help Desk, 513-556-HELP.

A note about UCit software

UC researchers are served with desktop software by UCIT. In many cases this software is licensed specifically to UC employees only (i.e., people who receive paychecks from UC) or must be run on UC-owned or controlled equipment, making it inaccessible to Cincinnati Children's personnel. Please make sure you read the license agreement carefully before you use UC software.

Faculty and students of UC are eligible to purchase software from UC. However, when purchasing from UC, the license agreement states that the software can be installed only on your personally owned or UC-owned computer and not on machines owned by other institutions. Since Children’s Hospital is a separate entity from UC, installing software purchased from UC on CCHMC owned computers is a violation of that license agreement. There is a difference in the price of software purchased from Biomedical Informatics at Children’s Hospital versus from the UC Bookstore. This difference is because UC qualifies for the educational discount whereas Children’s Hospital does not. Although Cincinnati Children’s Hospital is affiliated with UC, we are not a degree granting institution. We are a hospital, therefore we only qualify for the healthcare/non-profit discount.