GRR 1.2.1.41 – Detect Pedigree Errors

GRR 1.2.1.41

:: DESCRIPTION

GRR (Graphical Representation of Relationships) is a Windows-based application for detecting pedigree errors via graphically inspecting the distribution for marker allele sharing among pairs of family members or all pairs of individuals in a study.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

GRR

:: MORE INFORMATION

If you decide to use GRR, please take a minute to register.

CaTS 0.0.2 – Power Calculator for Two Stage Association Studies

CaTS 0.0.2

:: DESCRIPTION

CaTS is a simple, multi-platform interface for carrying out power calculations for large genetic association studies, including two stage genome wide association studies.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

CaTS

:: MORE INFORMATION

Citation:

Skol AD, Scott LJ, Abecasis GR and Boehnke M
Joint analysis is more efficient than replication-based analysis for two-stage genome-wide association studies.
Nat Genet (2006) 38:209-13

If you decide to use CaTS, please take a minute to register.

MERLIN 1.1.2 – Pedigree Analysis

MERLIN 1.1.2

:: DESCRIPTION

MERLIN (multipoint engine for rapid likelihood inference ) uses sparse trees to represent gene flow in pedigrees and is one of the fastest pedigree analysis packages around. it performs rapid haplotyping, genotype error detection and affected pair linkage analyses and can handle more markers than other pedigree analysis packages.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

MERLIN

:: MORE INFORMATION

Citation:

Abecasis GR, Cherny SS, Cookson WO and Cardon LR
Merlin-rapid analysis of dense genetic maps using sparse gene flow trees.
Nat Genet (2002) 30:97-101

If you decide to useMERLIN, please take a minute to register.

PSEUDO 0.3.5 – Evaluate Empirical P-values for Linkage Scans

PSEUDO 0.3.5

:: DESCRIPTION

PSEUDO is a program for fast evaluation of empirical p-values for linkage scans. It can evaluate the significance of any Kong and Cox lod score and is extremely efficient when compared to standard methods for the evaluation of empirical p-values.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

PSEUDO

:: MORE INFORMATION

Citation:

Wigginton JE and Abecasis GR (2006).
An evaluation of the replicate pool method: quick estimation of genome-wide linkage peak p-values.
Genet Epidemiol 30:320-32

If you decide to use PSEUDO, please take a minute to register.

FUGUE 0.2.3 – Haplotype Frequency Estimation

FUGUE 0.2.3

:: DESCRIPTION

FUGUE is the program used to construct haplotypes for the chromosome and linkage disequilibrium maps.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • MERLIN

:: DOWNLOAD

FUGUE

:: MORE INFORMATION

Citation:

Dawson E, Abecasis GR, Bumpstead S, Chen Y, Hunt S, Beare DM, Pabial J, Dibling T, Tinsley E, Kirby S, Carter D, Papaspyridonos M, Livingstone S, Ganske R, Lohmussaar E, Zernant J, Tonisson N, Remm M, Magi R, Puurand T, Vilo J, Kurg A, Rice K, Deloukas P, Mott R, Metspalu A, Bentley DR, Cardon LR and Dunham I
A first-generation linkage disequilibrium map of human chromosome
Nature (2002) 418:544-548

Phillips MS, Lawrence R, Sachidanandam R, Morris AP, Balding DJ, Donaldson MA, Studebaker JF, Ankener WM, Alfisi SV, Kuo FS, Camisa AL, Pazorov V, Scott KE, Carey BJ, Faith J, Katari G, Bhatti HA, Cyr JM, Derohannessian V, Elosua C, Forman AM, Grecco NM, Hock CR, Kuebler JM, Lathrop JA, Mockler MA, Nachtman EP, Restine SL, Varde SA, Hozza MJ, Gelfand CA, Broxholme J, Abecasis GR, Boyce-Jacino MT and Cardon LR
Chromosome-wide distribution of haplotype blocks and the role of recombination hot spots.
Nat Genet (2003) 33:382-7

PEDSTATS 0.6.12 – Statistics & Quality Assessments for Gene-mapping Data

PEDSTATS 0.6.12

:: DESCRIPTION

PEDSTATS is a handy tool for quick validation and summary of any pair of pedigree (.ped) and data (.dat) files.PEDSTATS produces summary statistics and basic quality assessments for gene-mapping data, accommodating either pedigree or case-control datasets.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

PEDSTATS

:: MORE INFORMATION

Citation:

Wigginton JE and Abecasis GR (2005)
PEDSTATS: descriptive statistics, graphics and quality assessment for gene mapping data
Bioinformatics 21:3445 – 3447.

If you decide to use PEDSTATS, please take a minute to register.

SNP-HWE – Routines for exact SNP tests of Hardy-Weinberg Equilibrium

SNP-HWE

:: DESCRIPTION

SNP-HWE (SNP tests of Hardy-Weinberg Equilibrium) is based on an efficient algorithm for enumerating the exact heterozygote probability distribution conditional on the number of minor alleles present in the sample. It adequately controls Type I error rates within large and small samples and is suitable for use in large-scale studies of SNP data. With appropriate citation, these routines are freely available for your use and can be incorporated into other programs.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • C++ Complier

:: DOWNLOAD

SNP-HWE

:: MORE INFORMATION

Citation:

Wigginton JE, Cutler DJ and Abecasis GR
A Note on Exact Tests of Hardy-Weinberg Equilibrium.
Am J Hum Genet (2005) 76: 887-93

If you decide to use SNP-HWE, please take a minute to register.

GOLD 1.1.0 – Graphical Overview of Linkage Disequilibrium

GOLD 1.1.0

:: DESCRIPTION

GOLD ( Graphical Overview of Linkage Disequilibrium) provides a graphical summary of linkage disequilibrium in human genetic data. The graphical summary is well suited to the analysis of dense genetic maps, where contingency tables are cumbersome to interpret. An interface to the Simwalk2 application allows for the analysis of family data.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

GOLD

:: MORE INFORMATION

If you decide to use GOLD, please take a minute to register.

QTDT 2.6.1 – Linkage Disequilibrium Analysis for Quantitative and Discrete Traits

QTDT 2.6.1

:: DESCRIPTION

QTDT (Quantitative and Discrete Traits) provides a convenient one-stop interface for family based tests of linkage disequilibrium. The general models can be used to analyse quantitative or discrete traits in nuclear families, with or without parental genotypes, or extended pedigrees. In addition, QTDT can calculate exact p-values by permutation even when multiple linked polymorphisms are tested.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

QTDT

:: MORE INFORMATION

Citation:

Abecasis GR, Cardon LR and Cookson WO
A General Test of Association for Quantitative Traits in Nuclear Families.
Am J Hum Genet (2000) 66:279-292

Abecasis GR, Cookson WO and Cardon LR
Pedigree tests of transmission disequilibrium.
Eur J Hum Genet (2000) 8:545-51

If you decide to use QTDT, please take a minute to register.

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.

If you decide to use MACH, please take a minute to register.