MaCH-Admix 2.0.203 – Genotype Imputation for Admixed Populations or with Large Reference Panels

MaCH-Admix 2.0.203

:: DESCRIPTION

MaCH-Admix is a genotype imputation software that extends the capabilities of MaCH. It has incorporated a novel piecewise reference selection method to create reference panels tailored for target individual(s).

::DEVELOPER

Yun Li Statistical Genetics Group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/ Windows/MacOsX

:: DOWNLOAD

 MaCH-Admix

:: MORE INFORMATION

Citation

MaCH-admix: genotype imputation for admixed populations.
Liu EY, Li M, Wang W, Li Y.
Genet Epidemiol. 2013 Jan;37(1):25-37. doi: 10.1002/gepi.21690. Epub 2012 Oct 16.

MIXSCORE 1.3 – Disease Scoring in Admixed Populations

MIXSCORE 1.3

:: DESCRIPTION

MIXSCORE is a software for disease scoring (combining case-only admixture and case-control SNP association signals) in Admixed Populations such as African Americans.

::DEVELOPER

Bogdan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MIXSCORE

:: MORE INFORMATION

Citation:

Pasaniuc et al. (2011).
Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a breast cancer consortium.
PLoS Genet. 2011 Apr;7(4):e1001371.

GEDI-ADMX 1.03 – GEDI for Admixed Populations

GEDI-ADMX 1.03

:: DESCRIPTION

GEDI-ADMX package provides methods for

local ancestry inference
SNP genotype error detection and correction
imputation of missing genotypes at typed SNPs, and
imputation of genotypes at untyped SNPs
in admixed populations based on whole-genome SNP genotype data and reference haplotype panels for ancestral populations.

::DEVELOPER

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

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

GEDI-ADMX for linux ; for windows

:: 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,