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Haplotype association software tools | Genome-wide association analysis

Recent literature has highlighted the advantages of haplotype association methods for detecting rare variants associated with common diseases. Source text: Datta and Biswas, 2015.

THESIAS
Desktop

THESIAS Testing Haplotype Effects In Association Studies

Provides haplotype analysis in unrelated individuals that can treat…

Provides haplotype analysis in unrelated individuals that can treat quantitative, binary, survival and polychotomous phenotype analyses. THESIAS is a multiple-imputation algorithm that never assigns…

GHap
Desktop

GHap Genome-Wide Haplotyping

A package designed to call haplotypes from phased marker data. GHap R…

A package designed to call haplotypes from phased marker data. GHap R identifies the different haplotype alleles (HapAllele) present in the data and scores sample haplotype allele genotypes based on…

haplo.stats
Desktop

haplo.stats

A suite of R routines for the analysis of indirectly measured haplotypes. The…

A suite of R routines for the analysis of indirectly measured haplotypes. The statistical methods assume that all subjects are unrelated and that haplotypes are ambiguous (due to unknown linkage…

SKAT
Desktop

SKAT SNP-set (Sequence) Kernel Association Test

A SNP-set (e.g., a gene or a region) level test for association between a set…

A SNP-set (e.g., a gene or a region) level test for association between a set of rare (or common) variants and dichotomous or quantitative phenotypes. SKAT aggregates individual score test statistics…

GENEBPM
Desktop

GENEBPM

A flexible Bayesian framework for modeling haplotype association with disease…

A flexible Bayesian framework for modeling haplotype association with disease in population-based studies of candidate genes or small candidate regions. Under this model, haplotypes are clustered…

WHaIT
Desktop

WHaIT Weighted Haplotype and Imputation-based Tests

A weighted haplotype-based approach and an imputation-based approach, to test…

A weighted haplotype-based approach and an imputation-based approach, to test for the effect of rare variants with GWAS data. Both methods can incorporate external sequencing data when available. We…

BOOGIE
Desktop

BOOGIE

A fast predictor for the inference of blood groups from single nucleotide…

A fast predictor for the inference of blood groups from single nucleotide variant (SNV) databases. BOOGIE correctly predicted the blood group with 94% accuracy for the Personal Genome Project whole…

Diplotyper
Desktop

Diplotyper

Combines an algorithm designed to cluster haplotypes of interest from a given…

Combines an algorithm designed to cluster haplotypes of interest from a given set of haplotypes with two existing tools: Haploview, for analyses of linkage disequilibrium blocks and haplotypes, and…

T-Trees
Desktop

T-Trees Trees inside Trees

A tree-based ensemble method that takes into account the correlation structure…

A tree-based ensemble method that takes into account the correlation structure among the genetic markers implied by linkage disequilibrium in GWAS data. In terms of risk prediction, we show…

hapassoc
Desktop

hapassoc

Inference of trait associations with SNP haplotypes and other attributes using…

Inference of trait associations with SNP haplotypes and other attributes using the EM algorithm. The R functions are used for inference of trait associations with haplotypes and other covariates in…

rGLM
Desktop

rGLM

A generalized linear model with regularization approach for detecting…

A generalized linear model with regularization approach for detecting disease-haplotype association using unphased single nucleotide polymorphisms data that is applicable to both common…

BhGLM
Desktop

BhGLM

An efficient and robust method to tackle these problems based on a Bayesian…

An efficient and robust method to tackle these problems based on a Bayesian hierarchical generalized linear model. Our model simultaneously fits environmental effects, main effects of numerous common…

LBL
Desktop

LBL Logistic Bayesian LASSO

An R package that performs Logistic Bayesian Lasso for finding association of…

An R package that performs Logistic Bayesian Lasso for finding association of SNP haplotypes and environmental factors with a trait in a case-control setting. Bayesian lasso is used to find the…

HaploBlockFinde…
Web
Desktop

HaploBlockFinder

A package for haplotype block identification, visualization and haplotype…

A package for haplotype block identification, visualization and haplotype tagging single nucleotide polymorphism (htSNP) selection. HaploBlockFinder can also compare the haplotype block structure…

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