BEAGLE specifications


Unique identifier OMICS_00052
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format VCF
Output data Variant calls
Output format VCF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Advanced
Version 4.0
Stability Stable
Maintained Yes



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  • person_outline Brian L. Browning <>

BEAGLE article

BEAGLE citations

PMCID: 5054554

[…] location (umd 3.1), (4) when the snp genotypes were not in hardy–weinberg equilibrium (p > 10−6). however, for the xp-ehh and fst tests, loci with a maf lower than 0.05 were also included. beagle (version 3.3.2) [22] was used to impute missing genotypes and infer the haplotype phase. to ensure independence among the individuals collected in both populations, a relatedness test […]

PMCID: 4283659

[…] each haplotype was considered as an independent sample, so that haplotypes belonging to the same individual do not necessarily need to cluster together. because missing sites were imputed with beagle, no missing alleles were present in the phased haplotypes. sites with more than two alleles were removed from the data and a distance matrix was constructed in plink (purcell et al., 2007). […]

PMCID: 3828151

[…] admixed trios. we first performed a genome-wide pairwise ibs estimation using plink [39] to ensure that the dataset contains no samples with more than 10% ibs with any other sample. then we used fastibd [37] to phase the data and estimate segments shared ibd longer than 2 mb to eliminate false positive ibd matches and assuming that ancestry will be shared among pairwise ibd hits of segments […]

PMCID: 3489600

[…] three methods: ld-block-based method by haploview, exhaustive variable-sized sliding window strategy by plink, and localized haplotype clustering approach by beagle. of all these approaches, only beagle identified a marginally significant (pemp = 0.0763) haplotype cluster (0.g) for rs220168 (s47) for sample set 1 with cases defined by se ≤ -12 d. further analysis showed that three snps […]

BEAGLE institution(s)
Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA

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