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

• 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.

Required Modules

Serial

• Beagle

System Variables

• HPC_{{#uppercase:Beagle}}_DIR
• HPC_{{#uppercase:Beagle}}_BIN
• HPC_{{#uppercase:Beagle}}_DOC
• HPC_{{#uppercase:Beagle}}_EXAMPLE

Citation

If you use BEAGLE in a published analysis, please report the BEAGLE version used and cite the appropriate publication or publications listed below.

BEAGLE's fastIBD method is described in

• B L Browning and S R Browning (2011) A fast, powerful method for detecting identity by descent. The American Journal of Human Genetics 88:173-182.

BEAGLE's methods for detecting homozygosity-by-descent and identity-by-descent are described in

• S R Browning and B L Browning (2010) High-resolution detection of identity by descent in unrelated individuals. The American Journal of Human Genetics 86:526-539. [link to article]

BEAGLE's methods for calling genotypes from genotype likelihood data are described in

• B L Browning and Z Yu (2009) Simultaneous genotype calling and haplotype phase inference improves genotype accuracy and reduces false positive associations for genome-wide association studies. The American Journal of Human Genetics 85:847-861.

BEAGLE's methods for imputing ungenotyped markers and phasing parent-offspring trios are described in

• B L Browning and S R Browning (2009) A unified approach to genotype imputation and haplotype phase inference for large data sets of trios and unrelated individuals. Am J Hum Genet 84:210-223.

BEAGLE's methods for inferring haplotype phase or sporadic missing data in unrelated individuals are described in

• S R Browning and B L Browning (2007) Rapid and accurate haplotype phasing and missing data inference for whole genome association studies using localized haplotype clustering. Am J Hum Genet 81:1084-1097.

BEAGLE's methods for association testing are described in

• B L Browning and S R Browning (2007) Efficient multilocus association mapping for whole genome association studies using localized haplotype clustering. Genet Epidemiol 31:365-375.

BEAGLE's haplotype frequency model was first described in:

• S R Browning (2006) Multilocus association mapping using variable-length Markov chains. Am J Hum Genet 78:903-13.