GwasTools Tools for Genome Wide Association studies

Notes:

This page collects resources for the people working in this platform.

Genetic association analyses are often compromised by missing genotypic data. However several imputation methods are available to overcome this in some way. Below an overview of some of the imputation methods that are published.

Category	Source	Description	Performance experience
Imputation	MACH	MACH 1.0 is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.	(pubmed)
Imputation	fastPHASE	The program fastPHASE implements methods for estimating haplotypes and missing genotypes from population SNP genotype data.	(pubmed)
Imputation	IMPUTE	IMPUTE is a program for imputing unobserved genotypes in genome-wide case-control studies based on a set of known haplotypes (like the HapMap Phase II haplotypes).	(pubmed)
Imputation	PLINK	PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.	(pubmed)
Imputation	Beagle	BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples.	(pubmed)