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BEAGLE specifications


Unique identifier OMICS_00052
Alternative name fastIBD
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input format VCF
Output data Some variant calls.
Output format VCF
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
License GNU General Public License version 3.0
Computer skills Advanced
Version 5.0
Stability Stable
Maintained Yes


  • FastIBD




No version available



  • person_outline Brian L. Browning <>

Publications for BEAGLE

BEAGLE citations


Genome wide scan reveals population stratification and footprints of recent selection in Nelore cattle

PMCID: 5930444
PMID: 29720080
DOI: 10.1186/s12711-018-0381-2

[…] [see additional file : table s2]. next, imputation of missing genotypes and haplotype phasing were performed by combining all the samples together, regardless of their respective line, using beagle software (version 3.3.2) []., two different methods were used to assess population stratification. first, a multidimensional scaling (mds) analysis was applied using the genomic distance […]


A survey of functional genomic variation in domesticated chickens

PMCID: 5902831
PMID: 29661130
DOI: 10.1186/s12711-018-0390-1

[…] to 60 k genotypes, to match 60 k-based haplotypes to the available sequence data. the software confirm-gt [] was used to match chromosome, strand, and allele to the phased 60 k reference population. beagle version 4.0 was used for imputation and phasing. carriers of haplotypes that were significantly depleted of homozygotes were examined for causal variants by selecting protein-altering variants […]


Trends in genome wide and region specific genetic diversity in the Dutch Flemish Holstein–Friesian breeding program from 1986 to 2015

PMCID: 5896142
PMID: 29642838
DOI: 10.1186/s12711-018-0385-y

[…] crv custom-made 60 k illumina panel (versions v1 and v2). genotypes were imputed to ~ 76 k from the different panels, following druet et al. [], and haplotypes were constructed with a combination of beagle [] and phasebook [], by exploiting both familial and population information. prior to imputation, snps with a call rate lower than 0.85, a maf lower than 0.025 or a difference larger than 0.15 […]


Detection of Selection Signatures in Chinese Landrace and Yorkshire Pigs Based on Genotyping by Sequencing Data

PMCID: 5900008
PMID: 29686696
DOI: 10.3389/fgene.2018.00119

[…] 0.95, (4) removing snps loci with hardy weinberg balance test less than 10-6 and (5) removing snps loci in sex chromosomes. following the quality control, the missing genotypes was imputed using the beagle (). after imputation, the average estimated squared correlation (r2) between the allele dosage with highest posterior probability and the true allele dosage fore the marker is 0.9982. […]


Comparison of phasing strategies for whole human genomes

PMCID: 5903673
PMID: 29621242
DOI: 10.1371/journal.pgen.1007308

[…] that belong to different parts of the genome. data for the phased moleculo na12878 genome were downloaded from the illumina basespace website (steemers, illumina, inc. personal communication) []., beagle (version 4.0 r1399). this computational phasing algorithm represents one of the early hmm-based approaches. it essentially samples different possible haplotype arrangements to find […]


Hybridization and gene flow in the mega pest lineage of moth, Helicoverpa

PMCID: 5948968
PMID: 29610329
DOI: 10.1073/pnas.1718831115

[…] a more complete dataset was used for subsequent analyses, whereby phasing and imputation of missing bases was performed on all snps from all samples using default parameters in beagle (). linkage disequilibrium (ld)-based pruning conducted using plink v. 1.07 () was used to filter one of a pair of snps using a pairwise ld threshold (r2 = 0.5) within windows of 50 snps, […]

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BEAGLE institution(s)
Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA; Department of Biostatistics, University of Washington, Seattle, WA, USA
BEAGLE funding source(s)
Supported by the National Human Genome Research Institute of the National Institutes of Health under Award Number R01HG008359.

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