Table 3.

List of Software Packages for Rare-Variant Association Tests

Name	Type	Methods Implemented	URL
EPACTS	stand alone	burden, MB test, SKAT, SKAT-O, VT	http://genome.sph.umich.edu/wiki/EPACTS
GRANVIL	stand alone	ARIEL, MZ	http://www.well.ox.ac.uk/GRANVIL
MiST	R-package	SKAT, MiST	http://cran.r-project.org/web/packages/MiST
PLINK/SEQ	stand alone	burden, C-alpha test, SKAT, SKAT-O, VT	http://atgu.mgh.harvard.edu/plinkseq
Rvtests	stand alone	burden, VT, KBAC method, SKAT	http://genome.sph.umich.edu/wiki/Rvtests
SCORE-Seq	stand alone	burden, SKAT, EREC test, VT, WSS	http://dlin.web.unc.edu/software/score-seq
SKAT	R-package	burden, SKAT, SKAT-O	http://www.hsph.harvard.edu/skat, http://cran.r-project.org/web/packages/SKAT
VAT	stand alone	aSum, burden, C-alpha test, KBAC method, RBT, VT	http://varianttools.sourceforge.net/Association/HomePage
Software Packages for Meta-analysis
MASS	stand alone	meta-analysis: burden, SKAT, VT	http://dlin.web.unc.edu/software/mass
MetaSKAT	R-package	meta-analysis: burden, SKAT, SKAT-O	http://www.hsph.harvard.edu/skat, http://cran.r-project.org/web/packages/MetaSKAT
seqMeta	R-package	meta-analysis: burden, SKAT, SKAT-O	http://cran.r-project.org/web/packages/seqMeta/
RAREMETAL	stand alone	meta-analysis: burden, SKAT, VT	http://genome.sph.umich.edu/wiki/RAREMETAL

Abbreviations are as follows: ARIEL, accumulation of rare variants integrated and extended locus-specific; aSum, data-adaptive sum test; EPACTS, efficient and parallelizable association container toolbox; EREC, estimated regression coefficient; GRANVIL, gene- or region-based analysis of variants of intermediate and low frequency; KBAC, kernel-based adaptive cluster; MASS, meta-analysis of sequencing studies; MB, Madsen and Browning; MiST, mixed-effects score test for continuous outcomes; RBT, replication-based test; Rvtests, rare-variant tests; SKAT, sequence kernel association test; VAT, variant association tools; VT, variable threshold; and WSS, weighted-sum statistic.