Tag: Linkage Disequilibrium

BEAGLECALL 1.0.1 – Genotype Calling using Linkage Disequilibrium for unrelated individuals

BEAGLECALL 1.0.1

:: DESCRIPTION

BEAGLECALL is a software package for simultaneous genotype calling and haplotype phasing for unrelated individuals.  BEAGLECALL produces output posterior genotype probabilities and output phased haplotypes.  BEAGLECALL generates extremely accurate genotype calls because it uses both allele signal intensity data and inter-marker correlation to call genotypes.  BEAGLECALL is designed for use with high-density SNP arrays, and it uses the BEAGLE haplotype frequency model to model inter-marker correlation.

::DEVELOPER

Brian L. Browning 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 BEAGLECALL

:: MORE INFORMATION

Citation:

Browning B, Yu Z. (2009)
Simultaneous genotype calling and haplotype phase inference improves genotype accuracy and reduces false positive associations for genome-wide association studies.
The American Journal of Human Genetics 85:847-861.

varLD 1.0 – Comparison of Variation in Linkage Disequilibrium between Population

varLD 1.0

:: DESCRIPTION

varLD can be used to perform inter-population comparison of regional patterns of linkage disequilibrium (LD), and quantifies which genomic regions carry dissimilar patterns of LD across the populations compared.

::DEVELOPER

Saw Swee Hock School of Public Health

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsXR package
  • Java

:: DOWNLOAD

  varLD

:: MORE INFORMATION

Citation:

varLD: a program for quantifying variation in linkage disequilibrium patterns between populations.
Ong RT, Teo YY.
Bioinformatics. 2010 May 1;26(9):1269-70. doi: 10.1093/bioinformatics/btq125. Epub 2010 Mar 22.

snp.plotter 0.5.1 – SNP/haplotype Association and Linkage Disequilibrium plotting package

snp.plotter 0.5.1

:: DESCRIPTION

snp.plotter is an R package that creates publishable-quality plots of p-values using single SNP and/or haplotype data. Main features of the package include options to display a linkage disequilibrium (LD) plot and the ability to plot multiple sets of results simultaneously. Plots can be created using global and/or individual haplotype p-values along with single SNP p-values.

::DEVELOPER

Augustin Luna, Kristin Nicodemus (email: augustin@mail.nih.gov)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 snp.plotter

:: MORE INFORMATION

Citation

Luna, Nicodemus (2007),
“snp.plotter: an R-based SNP/haplotype association and linkage disequilibrium plotting package“,
Bioinformatics, 23(6):774-776.

SIMLD 1.0 – Simulate Linkage Disequilibrium

SIMLD 1.0

:: DESCRIPTION

SIMLD is a software package to simulate realistic linkage disequilibrium patterns based on HapMap data

::DEVELOPER

Xiguo Yuan 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 SIMLD

:: MORE INFORMATION

Citation

Biochem Genet. 2011 Jun;49(5-6):395-409. doi: 10.1007/s10528-011-9416-x. Epub 2011 Jan 14.
Simulating linkage disequilibrium structures in a human population for SNP association studies.
Yuan X1, Zhang J, Wang Y.

BALD – Bayesian Analysis of Linkage Disequilibrium Differences

BALD

:: DESCRIPTION

BALD is a Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals.

::DEVELOPER

PathogenSeq

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 BALD

:: MORE INFORMATION

Citation

A Bayesian approach using covariance of single nucleotide polymorphism data to detect differences in linkage disequilibrium patterns between groups of individuals.
Clark TG, Campino SG, Anastasi E, Auburn S, Teo YY, Small K, Rockett KA, Kwiatkowski DP, Holmes CC.
Bioinformatics. 2010 Aug 15;26(16):1999-2003. Epub 2010 Jun 16.

BALD 0.2.1 – Blockwise Approach using Linkage Disequilibrium

BALD 0.2.1

:: DESCRIPTION

BALD is the R package BALD implements/combines functions for Genome-Wide Association Studies including simulation of SNPs data, constrained hierarchical clustering using Linkage Disequilibrium (LD) measures, the Gap statistic to find the optimal number of clusters, and statistical regression models for SNP selection (Univariate, Lasso, Group Lasso, Elastic-Net).

::DEVELOPER

Laboratoire de Mathématiques et Modélisation d’Évry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 BALD

:: MORE INFORMATION

Citation

Performance of a blockwise approach in variable selection using linkage disequilibrium information.
Dehman A, Ambroise C, Neuvial P.
BMC Bioinformatics. 2015 May 8;16:148. doi: 10.1186/s12859-015-0556-6.

LOCO-LD – LOcalization COrrected for Linkage Disequilibrium

LOCO-LD

:: DESCRIPTION

LOCO-LD is a method for the geographic localization of individuals. It takes as input genotype data and generates, for each individual, an estimate for their geographic coordinates of origin.

::DEVELOPER

Bogdan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • C Compiler
  • Matlab

:: DOWNLOAD

 LOCO-LD

:: MORE INFORMATION

Citation:

Enhanced Localization of Genetic Samples through Linkage-Disequilibrium Correction
Yael Baran, Inés Quintela, ángel Carracedo, Bogdan Pasaniuc, Eran Halperin
The American Journal of Human Genetics – 6 June 2013 (Vol. 92, Issue 6, pp. 882-894)

EH 24 – Estimate Linkage Disequilibrium between Different Markers

EH 24

:: DESCRIPTION

EH is a program to test and estimate linkage disequilibrium between different markers or between a disease locus and markers. This is an updated version in which the previous “disease” (case-control) option has been deleted (but see below how to work with case-control data).

::DEVELOPER

Lab of Statistical Genetics, Rockefeller University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 EH

:: MORE INFORMATION

References

Marchini J et al (2006) A comparison of phasing algorithms for trios and unrelated individuals. Am J Hum Genet 78, 437-450

Xie X, Ott J (1993) Testing linkage disequilibrium between a disease gene and marker loci. Am J Hum Genet 53, 1107 (abstract)

Terwilliger J, Ott J (1994) Handbook of Human Genetic Linkage. Johns Hopkins University Press, Baltimore

Volume Measures – Volume Measures for Linkage Disequilibrium

Volume Measures

:: DESCRIPTION

Volume Measures is the C code for calculating a number of volume measures of linkage disequilibrium.

::DEVELOPER

Yuguo Chen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOSX / Linux
  • C Compiler

:: DOWNLOAD

 Volume Measures

:: MORE INFORMATION

Citation

Chen, Y., C. Lin, C. Sabatti (2006)
“Volume Measures for Linkage Disequilibrium,”
BMC Genetics 7:54.

LD-Plus – Display of Single SNP Statistics in the Context of Linkage Disequilibrium and Haplotype Structures

LD-Plus

:: DESCRIPTION

LD-Plus is a data visualization application for the display of single SNP statistics in the context of linkage disequilibrium and haplotype structures. LD-Plus can display both continuous and categorical SNP statistics, and is designed to parse Haploview output to display both D’ and r2 LD plots, called or user-defined haplotype blocks, and haplotype frequencies. This web application will run Haploview and use the output to generate the plots.

::DEVELOPER

Ritchie Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux/Windows/MacOsX
  • Ruby

:: DOWNLOAD

 LD-Plus

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Feb 15;26(4):578-9. Epub 2010 Feb 3.
Visualizing SNP statistics in the context of linkage disequilibrium using LD-Plus.
Bush WS, Dudek SM, Ritchie MD.