Rare variant association software tools | Genome-wide association study data 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.
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 of SNPs in a SNP set and efficiently computes SNP-set level p-values, e.g. a gene or a region level p-value, while adjusting for covariates, such as principal components to account for population stratification. SKAT also allows for power/sample size calculations for designing for sequence association studies.
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 families, sibships, pedigrees, or any combination; (2) analyze dichotomous, measured, or time-to-onset traits and multiple traits; and (3) analyze markers on the x-chromosome with same options as autosomal marker analysis. It provides a way to proceed to bi-allelic and multi-allelic tests of association using standard genetic models.
Computes various statistical tests for discovering genome-wide association from sequence data. EPACTS provides a user-friendly interface for both scientific analysts and method developers. It supports as input an association mapping containing individual genotype information. This tool can automatically identify binary phenotypes and encode them into 1/2 values.
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 supported. It includes a variety of association tests (e.g. single variant score test, burden test, variable threshold test, SKAT test, fast linear mixed model score test). RVTESTS also provides useful companion features for annotating sequence variants, integrating bioinformatics databases, performing data quality control and sample selection.
Investigates genetic variants association with quantitative traits in family data. fanSKAT consists of an extension of sequence kernel association test (SKAT). It can be applied to quantitative traits with unknown or known heritability. This tool can be combined with the collapsing of some very rare genetic variants such as singletons. It is useful for common variant analysis, combined common and rare variant analysis or conditional association analyses.
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 triads. Besides, the software allows users to estimate effects of maternal haplotypes and parent-of-origin effects as well as special models, like X-inactivation.
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 features such as genes, pathways, evolutionary conserved regions, protein families, regulatory regions, and others based on user-designated parameters. BioBin provides the infrastructure to create complex and interesting hypotheses in an automated fashion thereby circumventing the necessity for advanced and time consuming scripting.