HARE – Harmonizing Genetic Ancestry and self-identified Race/Ethnicity

HARE

:: DESCRIPTION

HARE is an algorithm that defines GWAS analysis strata by harmonizing participants’ self-reported race/ethnicity and genetic ancestry.

:: DEVELOPER

Tang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package

:: DOWNLOAD

HARE

:: MORE INFORMATION

Citation

Fang H, et al.
Harmonizing Genetic Ancestry and Self-identified Race/Ethnicity in Genome-wide Association Studies.
Am J Hum Genet. 2019 Oct 3;105(4):763-772.

GAGA – Genetic Algorithm for Genetic Ancestry Method

GAGA

:: DESCRIPTION

GAGA is a program developed to partition a distance matrix between pairs of objects into K clusters in order to minimize the amount of mean differences within each group (SSD'(WP) statistic).

::DEVELOPER

Dept Genetic Identification ErasmusMC Rotterdam

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux
  • Java

:: DOWNLOAD

 GAGA

:: MORE INFORMATION

Citation

GAGA: a new algorithm for genomic inference of geographic ancestry reveals fine level population substructure in Europeans.
Lao O, Liu F, Wollstein A, Kayser M.
PLoS Comput Biol. 2014 Feb 20;10(2):e1003480. doi: 10.1371/journal.pcbi.1003480.

SNPWEIGHTS 2.1 – Inferring Genome-wide Genetic Ancestry using SNP Weights

SNPWEIGHTS 2.1

:: DESCRIPTION

SNPweights is a software package for inferring genome-wide genetic ancestry using SNP weights precomputed from large external reference panels

::DEVELOPER

Alkes Price

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 SNPweights

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Jun 1;29(11):1399-406. doi: 10.1093/bioinformatics/btt144. Epub 2013 Mar 28.
Improved ancestry inference using weights from external reference panels.
Chen CY, Pollack S, Hunter DJ, Hirschhorn JN, Kraft P, Price AL.

GemTools – Estimate Genetic Ancestry

GemTools

:: DESCRIPTION

GemTools provides computationally efficient tools for modeling genetic ancestry based in the SNP information.  GemTools is a package of functions to help the user account for genetic ancestry of a large number of individuals using spectral graph theory and projections to break a large problem into smaller pieces and calculate genetic ancestry information efficiently, i.e., a divide and conquer (dac) strategy.

::DEVELOPER

COMPUTATIONAL GENETICS LAB At the UNIVERSITY OF PITTSBURGH MEDICAL CENTER

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

  GemTools

:: MORE INFORMATION

Citation:

Rosenberg, N., Pritchard, J., Weber, J., Cann, H., Kidd, K., Zhivotovsky, L., and Feldman, M. (2002).
Genetic structure of human populations.
Science, 298, 2381–2385.