BEAGLE

Description

beagle website

BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can perform the following: * Phase genotype data (i.e. infer haplotypes) for unrelated individuals, parent-offspring pairs, and parent-offspring trios. * Infer sporadic missing genotype data. * Impute ungenotyped markers that have been genotyped in a reference panel. perform single marker and haplotypic association analysis. * Detect genetic regions that are homozygous-by-descent in an individual or identical-by-descent in pairs of individuals. Beagle can also be used in conjunction with PRESTO, a program for fast and flexible permutation testing. PRESTO can compute empirical distributions of order statistics, analyze stratified data, and determine significance levels for one-stage and two-stage genetic association studies.

Environment Modules

Run module spider beagle to find out what environment modules are available for this application.

Environment Variables

• HPC_BEAGLE_DIR - installation directory
• HPC_BEAGLE_BIN - executable directory
• HPC_BEAGLE_DOC - documentation directory

Categories

biology, genomics