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IMPUTE and other GWA tools


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


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