EMINIM 1.01 – Expectation-Maximized INtegreative IMputation

EMINIM 1.01

:: DESCRIPTION

EMINIM is a software for imputation of unobserved genotypes using a set of reference haplotype panel at a higher-density SNP set such as HapMap, and lower-density genotypes of a target individual using such as genotyping arrays. Our method is adaptive in the sense that it learns transtition/emission parameters of hidden Markov model using EM algorithm with standard Poisson point process for modeling recombination. Our method is memory-efficient by efficiently utilizing silent states in the HMM. EMINIM provides interfaces both for human and inbred model organisms such as laboratory mice. Our method is demonstrated to have ten times smaller errors than the previous imputation method designed for inbred mouse for high-confidence genotypes.

::DEVELOPER

Hyun Min Kang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

EMINIM

:: MORE INFORMATION

Citation

J Comput Biol. 2010 Mar;17(3):547-60.
EMINIM: an adaptive and memory-efficient algorithm for genotype imputation.
Kang HM, Zaitlen NA, Eskin E.

BEAMimpute – Bayesian Epistatis Association Mapping via Imputation

BEAMimpute

:: DESCRIPTION

BEAMimpute (Bayesian Epistatis Association Mapping via Imputation) uses Markov Chain Monte Carlo (MCMC) to impute untyped SNPs and detect both single-marker and interaction effects from the imputed case-control SNP data.

::DEVELOPER

Yu Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

BEAMimpute

:: MORE INFORMATION

Citation

Nat Genet. 2007 Sep;39(9):1167-73. Epub 2007 Aug 26.
Bayesian inference of epistatic interactions in case-control studies.
Zhang Y, Liu JS.

WHaIT – Weighted Haplotype and Imputation dosage Tests

WHaIT

:: DESCRIPTION

WHaIT (Weighted Haplotype and Imputation dosage Tests) tests for the association of multiple rare variants with binary traits. It encompasses two sets of tests: a Weighted Haplotype test and an Imputation-based test.

::DEVELOPER

Yun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

WHaIT

:: MORE INFORMATION

Citation

Am J Hum Genet. 2010 Nov 12;87(5):728-35. Epub 2010 Nov 4.
To identify associations with rare variants, just WHaIT: Weighted haplotype and imputation-based tests.
Li Y, Byrnes AE, Li M.

RegionalHapMapExtractor – Extract a Region from HapMapII for MaCH imputation

RegionalHapMapExtractor

:: DESCRIPTION

RegionalHapMapExtractor is a software to extract a region from hapMapII for MaCH imputation

::DEVELOPER

Yun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
Perl

:: DOWNLOAD

RegionalHapMapExtractor

:: MORE INFORMATION

GEDI 1.03 – Genotype Error Detection & Imputation

GEDI 1.03

:: DESCRIPTION

GEDI package provides methods for

* error detection in whole-genome SNP genotype data
* recovery of missing SNP genotypes
* imputation of genotypes at untyped SNPs based on reference haplotypes such as those provided by the Hapmap project
* genotype phasing through a copy of our highly scalable ENT algorithm.

GEDI handles genotype data from unrelated individuals as well as individuals related by simple pedigrees such as trios. GEDI computations rely on efficient likelihood computations based on a Hidden Markov Model of haplotype diversity in the population under study.

::DEVELOPER

Bioinformatics Lab , Computer Science & Engineering Dept. University of Connecticut

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Linux

:: DOWNLOAD

GEDI

:: MORE INFORMATION

Citation:

J. Kennedy and I.I. Mandoiu and B. Pasaniuc,
Genotype Error Detection using Hidden Markov Models of Haplotype Diversity,
Journal of Computational Biology 15, pp. 1155-1171, 2008,