Data management

• Read data in a variety of formats
• Recode and reorder files
• Merge two or more files
• Extracts subsets (SNPs or individuals)
• Flip strand of SNPs
• Compress data in a binary file format

Summary statistics for quality control

• Allele, genotypes frequencies, HWE tests
• Missing genotype rates
• Inbreeding, IBS and IBD statistics for individuals and pairs of individuals
• non-Mendelian transmission in family data
• Sex checks based on X chromosome SNPs
• Tests of non-random genotyping failure

Population stratification detection

• Complete linkage hierarchical clustering
• Handles virtually unlimited numbers of SNPs
• Multidimensional scaling analysis to visualise substructure
• Significance test for whether two individuals belong to the same population
• Constrain cluster solution by phenotype, cluster size and/or external matching criteria
• Perform subsequent association analyses conditional on cluster solution

Basic association testing

• Case/control
  • Standard allelic test
  • Fisher's exact test
  • Cochran-Armitage trend test
  • Mantel-Haenszel and Breslow-Day tests for stratified samples
  • Dominant/recessive and general models
  • Model comparison tests (e.g. general versus multiplicative)
• Family-based association (TDT, sibship tests)
• Quantitative traits, association and interaction
• Association conditional on one or more SNPs
• Asymptotic and empirical p-values
• Flexible clustered permutation scheme
• Analysis of genotype probability data and fractional allele coounts (post-imputation)

Multimarker predictors, haplotypic tests

• Suite of flexible, conditional haplotype tests
• Case/control and TDT association on the probabilistic haplotype phase
• A set of proxy associaiton" methods to study single SNP associations in their local haplotypic context
• Imputation heuristic, to test untyped SNPs given a reference panel

Copy number variant analysis

• Joint SNP and CNV tests for common copy number variants
• Filtering and summary procedures for segmental (rare) CNV data
• Case/control comparison tests for global CNV properties
• Permutation-based association procedure for identifying specific loci

Additional tests

• Gene-based tests of association
• Screen for epistasis
• Gene-environment interaction with continuous and dichotomous environments

Meta-analysis

• Automatically combine several generically-formatted summary files, for millions of SNPs
• Fixed and random effects models

Result annotation and reporting

• Post-analysis annotation of result files
• LD-based and region-based grouping of results across multiple studies

Additional features

• Extensible with via R function plug-ins
• Web-based SNP and gene annotation lookup feature
• Simple SNP simulation feature
• ID helper tools, for tracking and working with project data
• See the main documentation for full list of features