View source for 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.


{| class="wikitable sortable" border="1"
|-
! Category
! Source
! Description
! Performance experience
|-
| Imputation
| [http://www.sph.umich.edu/csg/abecasis/MACH/download/ MACH]
| MACH 1.0 is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.
| ([http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18958166 pubmed])
|-
| Imputation
| [http://depts.washington.edu/ventures/UW_Technology/Express_Licenses/fastPHASE.php fastPHASE]
| The program fastPHASE implements methods for estimating haplotypes and missing genotypes from population SNP genotype data. 
| ([http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18958166 pubmed])
|-
| Imputation
| [http://www.stats.ox.ac.uk/~marchini/software/gwas/impute.html 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).
| ([http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18958166 pubmed])
|-
| Imputation
| [http://pngu.mgh.harvard.edu/purcell/plink/download.shtml 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.
| ([http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18958166 pubmed])
|-
| Imputation
| [http://www.stat.auckland.ac.nz/~browning/beagle/beagle.html 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.
| ([http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=18958166 pubmed])
|}

[[Category:Biobanking / Tools]]