RAT (Rapid Association Test) is a software for testing association between single nucleotide polymorphisms (SNPs) and a disease. The main advantage of RAT is its ability to calculate accurately and quickly high significance disease association. For large data set and low p-values, RAT is 2-4 orders of magnitude faster than the standard permutation test.
OVPDT (Ordered Subset – Variable Threshold – Pedigree Disequilibrium Test) is a family-based association test using both common and rare variants and accounting for directions of effects for sequencing data.
OPTPDT (Optimal P-value Threshold Pedigree Disequilibrium Test)is a family-based multi-SNP association test. A variable p-value threshold algorithm is used in the test to select an optimal subset of SNPs that has the strongest association signals.
qMSAT is a powerful test that directly incorporates sequencing qualities in association tests with multiple rare variants. It allows for the adjustment of additional covariates and is robust towards the inclusion of noncausal variants and variants having effects with different magnitudes and directions. Furthermore, it can coherently account for missing genotypes and conjoin in a principled way individuals or variants sequenced at varying coverage depths.
RWAS (Rare variant Weighted Aggregate Statistic) is a groupwise association test for identifying associations of groups of rare variants. RWAS groups variants and computes a weighted sum of differences in mutation counts between case and control individuals. Weights of RWAS are estimated from data to achieve nearly optimal power under a disease model in which all variants make an equally small contribution to population disease risk.
LRT (Likelihood Ratio Test) is a method that tries to identify which variants are causal by taking advantage of both prior information (of how likely each variant is functional) and data. LRT uses this information (of which variants are likely causal) to better detect associations of groups of rare variants.
Jae Hoon Sul, Buhm Han, Eleazar Eskin.
“Increasing Power of Groupwise Association Test with Likelihood Ratio Test.”
In Proceedings of the Fifteenth Annual Conference on Research in Computational Biology (RECOMB-2011). Vancouver, Canada: March 28th-31st, 2011
AMELIA (Allele Matching Empirical Locus-specific Integrated Association) is a program that employs allele matching to analyse the effects of rare variants within a specific locus.
LCMT is a small program performing “combining” association test over multiple genetic markers.LCMT implements the “combining” method for the association test over multiple genetic markers. It optimally utilizes the information from those markers. It is preferred over several competing tests, such as the Bonferroni procedure, the permutation procedure, the traditional χ2 procedure, the regression procedure (Hotelling T2 test) and the haplotype-based test.