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Rare variant association software tools | Genome-wide association analysis

Although genome-wide association studies have been successful in detecting associations with common variants, there is currently an increasing interest in identifying low frequency and rare variants associated with complex traits. Source text: Li et…
Haplin
Desktop

Haplin

Analyzes genetic association of case-parent triad data with multiple markers.…

Analyzes genetic association of case-parent triad data with multiple markers. Haplin in an open source package which provides estimation based on haplotypes with complete or incomplete control…

buRden
Desktop

buRden

Provides an Rcpp package for performing "burden" tests of…

Provides an Rcpp package for performing "burden" tests of associations due to rare variants by permutation. buRden was used in a study that explores the impact of genetic model and…

MetaSKAT
Desktop

MetaSKAT

A general statistical framework for meta-analysis of gene- or region-based…

A general statistical framework for meta-analysis of gene- or region-based multimarker rare variant association tests in sequencing association studies. MetaSKAT can carry out meta-analysis of SKAT,…

iGasso
Desktop

iGasso

Provides a collection of statistical tests developed for genetic association…

Provides a collection of statistical tests developed for genetic association studies. iGasso contains functions for: (i) rare variants association, (ii) association with multiple phenotypes, (iii)…

SEQSpark
Desktop

SEQSpark

Provides an analysis method for large-scale sequence data quality control,…

Provides an analysis method for large-scale sequence data quality control, annotation, and rare variant association analysis. SEQSpark can be used for the analysis of large-scale genetic…

PreMeta
Desktop

PreMeta

Facilitates the exchange of information between software packages for…

Facilitates the exchange of information between software packages for meta-analysis of rare-variant associations. PreMeta reformats the output files of study-level summary statistics generated by…

DoEstRare
Desktop

DoEstRare Density-oriented Estimation for Rare variant positions

Allows to detect both global enrichment in rare alleles and localized clusters…

Allows to detect both global enrichment in rare alleles and localized clusters of disease-risk rare variants (DRVs). The DoEstRare statistic consists in comparing simultaneously the mutation position…

FREGAT
Desktop

FREGAT Family REGional Association Tests

An R package that can handle family and population samples and implements a…

An R package that can handle family and population samples and implements a wide range of region-based association methods including burden tests, functional linear models, and kernel machine-based…

RVTESTS
Desktop

RVTESTS Rare Variant TESTS

A flexible software package for genetic association studies. RVTESTS is…

A flexible software package for genetic association studies. RVTESTS is designed to support unrelated individual or related (family-based) individuals. Both quantitative trait and binary trait are…

RVFam
Desktop

RVFam Rare Variant association analysis with Family data

An R software package designed to analyze continuous, binary and survival…

An R software package designed to analyze continuous, binary and survival traits against rare and common sequencing variants in genome-wide association studies (GWAS) involving family data. Single…

Mutational…
Desktop

Mutational Spectrum

Investigates variation in the rare variant spectrum in a sample of human…

Investigates variation in the rare variant spectrum in a sample of human genomes representing all major world populations. Mutational was applied to TCC>TTC mutations in people from Western…

ZFA
Desktop

ZFA Zoom-Focus algorithm

Optimizes the testing region for any region-based rare variant association test…

Optimizes the testing region for any region-based rare variant association test as a wrapper function. ZFA is an algorithm that consists of two main steps: (i) Zooming, in which a fixed genomic…

BioBin
Desktop

BioBin

A package to automate the process of binning rare variants into groups for…

A package to automate the process of binning rare variants into groups for statistical association analysis using a biological knowledge-driven framework. BioBin collapses variants into biological…

SEQPower
Desktop

SEQPower

Provides statistical power analysis and sample size estimation for…

Provides statistical power analysis and sample size estimation for sequence-based association studies. SEQPower generates sequencing data using forward-time simulation while incorporating demographic…

MAMBA
Desktop

MAMBA

A computer program for the analysis and interpretation of genomics data with an…

A computer program for the analysis and interpretation of genomics data with an emphasis on understanding the genetic basis of biomedical traits. In MAMBA, statistical methods for the analysis of…

SimRare
Desktop

SimRare

An interactive program that integrates generation of rare variant…

An interactive program that integrates generation of rare variant genotype/phenotype data and evaluation of association methods using a unified platform. Variant data are generated for gene regions…

MARV
Desktop

MARV Multi-phenotype Analysis of Rare Variants

Provides analyses of all phenotype combinations within one run and calculates…

Provides analyses of all phenotype combinations within one run and calculates the Bayesian Information Criterion to facilitate model selection. MARV is based on a method that collapses rare variants…

VAT
Desktop

VAT Variant Association Tools

A developmental branch of variant tools expanding its scope from analyzing…

A developmental branch of variant tools expanding its scope from analyzing individual genomic variants to analyzing large sequence data (whole genome sequencing, whole exome sequencing) or exome…

AP-SKAT
Desktop

AP-SKAT Adaptive sequential kernel association test

An adaptive sequential kernel association test (SKAT) procedure which…

An adaptive sequential kernel association test (SKAT) procedure which classifies significant SNP sets and ranks them according to the permuted p-values. AP-SKAT stops the permutation test when the…

FFBSKAT
Desktop

FFBSKAT Fast Family-Based Sequence Kernel Association Test

An efficient tool for region/gene association analysis of quantitative traits…

An efficient tool for region/gene association analysis of quantitative traits in samples of related individuals. This software implements a score-based variance component test to assess the…

gTDT
Desktop

gTDT group-wise TDT

A haplotype-based framework for group-wise transmission/disequilibrium tests…

A haplotype-based framework for group-wise transmission/disequilibrium tests (TDT) that is flexible to encompass a variety of genetic models such as additive, dominant and compound heterozygous (CH)…

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…

SCORE-Seq
Desktop

SCORE-Seq

A command-line program which implements score statistics for detecting disease…

A command-line program which implements score statistics for detecting disease associations with rare variants in sequencing studies. The mutation information is aggregated across multiple variant…

qMSAT
Desktop

qMSAT quality-weighted Multivariate Score Association Test

Allows powerful association tests between complex traits and multiple rare…

Allows powerful association tests between complex traits and multiple rare variants under the presence of sequencing errors. qMSAT is a procedure that can increase power over existing methods under…

famFLM
Desktop

famFLM

A region-based association test for familial data under functional linear…

A region-based association test for familial data under functional linear models. famFLM increases the power of regional association analysis of quantitative traits compared with burden-based and…

FastSKAT
Desktop

FastSKAT

Provides a highly-accurate approximation of SKAT’s p-value with orders of…

Provides a highly-accurate approximation of SKAT’s p-value with orders of magnitude smaller computational burden than current methods. FastSKAT achieves this in part using recent advances in random…

FARVAT
Desktop

FARVAT FAmily-based Rare Variant Association Test

A statistical test for gene-based association test with related samples. FARVAT…

A statistical test for gene-based association test with related samples. FARVAT assumed that families were ascertained with the disease status of family members, and incorporation of the estimated…

FamLBL
Desktop

FamLBL Family-triad-based Logistic Bayesian Lasso

Estimates effects of haplotypes on complex diseases using SNP data. By choosing…

Estimates effects of haplotypes on complex diseases using SNP data. By choosing appropriate prior distribution, effect sizes of unassociated haplotypes can be shrunk toward zero, allowing for more…

PODKAT
Desktop

PODKAT POsition-Dependent Kernel Association Test

Supplies an association test which is able of dealing with variants (rare and…

Supplies an association test which is able of dealing with variants (rare and even). PODKAT makes it possible thanks to a kernel-based approach which takes the positions of the variants into account.…

seqMeta
Desktop

seqMeta

Meta-analysis of region-based tests of rare DNA variants. seqMeta computes…

Meta-analysis of region-based tests of rare DNA variants. seqMeta computes necessary information to meta-analyze region-based tests for rare genetic variants (e.g. SKAT, T1) in individual studies,…

famSKAT
Desktop

famSKAT family-based SKAT

An extension of sequence kernel association test (SKAT) that can be applied to…

An extension of sequence kernel association test (SKAT) that can be applied to data with familial correlation. famSKAT has a different test statistic and null distribution compared to SKAT, but is…

RVS
Desktop

RVS Rare Variant Sharing

Implements tests of association and linkage between rare genetic variant…

Implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype. RVS computes the ratio of difference between inferred and expected kinship coefficient…

RAREMETALWORKER
Desktop

RAREMETALWORKER

A tool for single variant analysis, generating summary statistics for gene…

A tool for single variant analysis, generating summary statistics for gene level meta-analyses in RAREMETAL.

EPACTS
Desktop

EPACTS Efficient and Parallelizable Association Container Toolbox

A versatile software pipeline to perform various statistical tests for…

A versatile software pipeline to perform various statistical tests for identifying genome-wide association from sequence data through a user-friendly interface, both to scientific analysts and to…

PLINK/SEQ
Desktop

PLINK/SEQ

An open-source C/C++ library for working with human genetic variation data. The…

An open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing…

PB-STAR
Desktop

PB-STAR

Analyzes rare variants segregated in pedigrees by using a family-based…

Analyzes rare variants segregated in pedigrees by using a family-based statistic. PB-STAR is developed to allow to compare affected and unaffected individuals into pedigrees according to their…

FBAT
Desktop

FBAT Family Based Association Test

Implements a broad class of Family Based Association Tests, adjusted for…

Implements a broad class of Family Based Association Tests, adjusted for population admixture. FBAT offers a wide range of functionalities that permit, for example, to (1) use data from nuclear…

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