Tag: Admixed Population

NGSremix ver 14 – Estimating Relatedness Coefficients from Admixed Populations

NGSremix ver 14

:: DESCRIPTION

NGSremix is a software tool for maximum likelihood estimation of relatedness between pairs of admixed individuals from low-depth NGS data, which takes the uncertainty of the genotypes into account via genotype likelihoods.

::DEVELOPER

NGSremix team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NGSremix

:: MORE INFORMATION

Citation

Nøhr AK, Hanghøj K, Erill GG, Li Z, Moltke I, Albrechtsen A.
NGSremix: A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data.
G3 (Bethesda). 2021 May 20;11(8):jkab174. doi: 10.1093/g3journal/jkab174. Epub ahead of print. PMID: 34015083; PMCID: PMC8496226.

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.

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.

bnpsd 1.2.3 – Model and Simulate Admixed Populations

bnpsd 1.2.3

:: DESCRIPTION

bnpsd (Balding-Nichols Pritchard-Stephens-Donnelly) is an R package to model and simulate admixed populations

::DEVELOPER

The Ochoa Lab 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • R

:: DOWNLOAD

bnpsd

:: MORE INFORMATION

Citation

Ochoa, Alejandro, and John D. Storey. 2016a.
“FST And Kinship for Arbitrary Population Structures I: Generalized Definitions.”
bioRxiv doi:10.1101/083915.

Ochoa, Alejandro, and John D. Storey. 2016b.
“FST And Kinship for Arbitrary Population Structures II: Method of Moments Estimators.”
bioRxiv doi:10.1101/083923.

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,