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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 resource, software application
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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The NIDDK Information Network (dkNET) serves the needs of basic and clinical investigators by providing seamless access to large pools of data and research resources relevant to the mission of The National Institute of Diabetes Digestive and Kidney Diseases (NIDDK). dkNET is hosted at University of California San Diego, and is supported by NIH NIDDK grant 2U24DK097771-09.
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