AlphaRecode – Recode Pedigree and Sort it

AlphaPeel is a software package for calling, phasing, and imputing genotype and sequence data in pedigree populations. This program implements single locus peeling, multi locus peeling, and hybrid peeling.

::DEVELOPER

AlphaGenes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/MacOsX

:: DOWNLOAD

AlphaPeel

:: MORE INFORMATION

Citation

Whalen A, Ros-Freixedes R, Wilson DL, Gorjanc G, Hickey JM.
Hybrid peeling for fast and accurate calling, phasing, and imputation with sequence data of any coverage in pedigrees.
Genet Sel Evol. 2018 Dec 18;50(1):67. doi: 10.1186/s12711-018-0438-2. PMID: 30563452; PMCID: PMC6299538.

Pedgene 3.3 – Gene-level Statistics for Pedigree Data

Pedgene 3.3

:: DESCRIPTION

Pedgene offers an R package that performs gene-level kernel and burden association tests for genetic variants with disease status and continuous traits for pedigree data and unrelated subjects.

::DEVELOPER

Statistical Genetics and Genetic Epidemiology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R

:: DOWNLOAD

Pedgene

:: MORE INFORMATION

Citation

Genet Epidemiol. 2013 Jul;37(5):409-18. doi: 10.1002/gepi.21727. Epub 2013 May 5.
Multiple genetic variant association testing by collapsing and kernel methods with pedigree or population structured data.
Schaid DJ1, McDonnell SK, Sinnwell JP, Thibodeau SN.

kinship2 1.8.5 – Pedigree Functions

kinship2 1.8.5

:: DESCRIPTION

kinship2 offers routines to handle family data with a pedigree object.

::DEVELOPER

Statistical Genetics and Genetic Epidemiology Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
R

:: DOWNLOAD

kinship2

:: MORE INFORMATION

Citation

Hum Hered. 2014;78(2):91-3. doi: 10.1159/000363105. Epub 2014 Jul 29.
The kinship2 R package for pedigree data.
Sinnwell JP1, Therneau TM, Schaid DJ.

MdrPDT 2.0.1.21 – Multifactor Dimensionality Reduction and genotype Pedigree Disequilibrium Test

MdrPDT 2.0.1.21

:: DESCRIPTION

MDR-PDT merges the MDR method with the genotype-Pedigree Disequilibrium Test (geno-PDT). MDR-PDT allows identification of single-locus effects or joint effects of multiple loci in families of diverse structure. We present simulations to demonstrate the validity of the test and evaluate its power. To examine its applicability to real data, we applied the MDR-PDT to data from candidate genes for Alzheimer disease (AD) in a large family dataset. These results show the utility of the MDR-PDT for understanding the genetics of complex diseases.

::DEVELOPER

Ritchie Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / MacOsX
Java

:: DOWNLOAD

MDR-PDT

:: MORE INFORMATION

Citation:

Martin, Ritchie, Hahn, Kang, Moore (2006),
“A novel method to identify gene-gene effects in nuclear families: the MDR-PDT“,
Genetic Epidemiology, 30:111-123.

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.

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.

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.

LAMP 0.0.12 – Linkage & Association Modeling for Pedigrees

LAMP 0.0.12

:: DESCRIPTION

LAMP (Linkage & Association Modeling for Pedigrees) uses a maximum likelihood model to extract information on genetic linkage and association from samples of unrelated individuals, sib pairs, trios and larger pedigrees (Li et al, 2005; Li et al, 2006). It provides estimates of genetic model parameters and powerful tests of association in settings where population stratification is not a concern.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Windows / Mac / Linux

:: DOWNLOAD

LAMP

:: MORE INFORMATION

Citation:

Li, Boehnke and Abecasis (2005).
Joint Modeling of Linkage and Association: Identifying SNPs Responsible for a Linkage
Signal. Am J Hum Genet 76:934-49

Li, Boehnke and Abecasis (2006).
Efficient study designs for test of genetic association using sibship data and unrelated cases and controls.
Am J Hum Genet 78:778-92

GIGI-Pick 1.06 – Subject Selection for Sequencing in Pedigrees

GIGI-Pick 1.06

:: DESCRIPTION

GIGI-Pick is a computer program that facilitates the evaluation and comparison of subject selection choices in sequencing studies in pedigrees.

::DEVELOPER

Ellen M. Wijsman

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler

:: DOWNLOAD

GIGI-Pick

:: MORE INFORMATION

Citation:

Cheung CYK, Blue EM, Wijsman EM (2014)
A statistical framework to guide sequencing choices in pedigrees.
American Journal of Human Genetics 94:257-267.