URL: http://faculty.washington.edu/browning/beagle/beagle.html
Proper Citation: BEAGLE (RRID:SCR_001789)
Description: Software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. BEAGLE can * 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. BEAGLE is written in Java and runs on any computing platform with a Java version 1.6 interpreter (e.g. Windows, Unix, Linux, Solaris, Mac).
Abbreviations: BEAGLE
Synonyms: BEAGLE Genetic Analysis Software Package
Resource Type: software application, software resource
Defining Citation: PMID:17924348, PMID:17326099, PMID:21310274, DOI:10.1086/521987
Keywords: gene, genetic, genomic, java, ms-windows, linux, unix, solaris, macos, identity by descent, genotype, haplotype
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