IMPUTE 5 v1.1.5- Genotype Imputation in Genome-wide Association Study

IMPUTE 5 v1.1.5

:: DESCRIPTION

IMPUTE is a program for estimating (“imputing”) unobserved genotypes in SNP association studies. The program is designed to work seamlessly with the output of the genotype calling program CHIAMO and the population genetic simulator HAPGEN, and it produces output that can be analyzed using the program SNPTEST.

::DEVELOPER

Jonathan Marchini

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows /MacOsX / Linux

:: DOWNLOAD

IMPUTE

:: MORE INFORMATION

Citation

Rubinacci S, Delaneau O, Marchini J.
Genotype imputation using the Positional Burrows Wheeler Transform.
PLoS Genet. 2020 Nov 16;16(11):e1009049. doi: 10.1371/journal.pgen.1009049. PMID: 33196638; PMCID: PMC7704051.

B. N. Howie, P. Donnelly and J. Marchini (2009)
A flexible and accurate genotype imputation method for the next generation of genome-wide association studies.
PLoS Genetics 5(6): e1000529

mendel-gpu – GPU enabled Haplotying and Genotype Imputation

mendel-gpu

:: DESCRIPTION

mendel-gpu uses OpenCL kernels to rapidly impute genotypes using linkage disequilibrium patterns in unrelated subjects. It is appropriate for resequencing data.

::DEVELOPER

Gary K. Chen, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ compiler

:: DOWNLOAD

mendel-gpu

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Nov 15;28(22):2979-80. doi: 10.1093/bioinformatics/bts536. Epub 2012 Sep 5.
Mendel-GPU: haplotyping and genotype imputation on graphics processing units.
Chen GK1, Wang K, Stram AH, Sobel EM, Lange K.

MACH 1.0 – Haplotyping, Genotype Imputation & Disease Association Analysis

MACH 1.0

:: DESCRIPTION

MACH (Markov Chain Haplotyping) is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Windows / Mac / Linux

:: DOWNLOAD

MACH

:: MORE INFORMATION

Citation:

Li Y, Willer CJ, Ding J, Scheet P and Abecasis GR (2006)
MaCH: using sequence and genotype data to estimate haplotypes and unobserved genotypes.
Genet Epidemiol 34:816-834.

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