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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


Dissecting closely linked association signals in combination with the mammalian phenotype database can identify candidate genes in dairy cattle

BMC Genet
PMCID: 5948690
PMID: 29751743
DOI: 10.1186/s12863-018-0620-0

[…] utation methods rely on unambiguous sequences of variants. Positions with disagreements between alleles for sequence and HD data were also deleted. Reference genotype probability data was run through BEAGLE [] and all markers with an R2 value (squared correlation between the true and imputed allele dosages) below 0.9 were removed from the original sequence data. This was done in order to remove po […]


Genome wide association meta analysis of circulating odd numbered chain saturated fatty acids: Results from the CHARGE Consortium

PLoS One
PMCID: 5940220
PMID: 29738550
DOI: 10.1371/journal.pone.0196951
call_split See protocol

[…] PIVUS: Illumina OmniExpress and CardioMetabochip). Samples with call rates <95–97% at genotyped markers were excluded. Genotypes were imputed to approximately 2.5 million HapMap SNPs by using either BEAGLE[] (CARDIA), BIMBAM[] (CHS), IMPUTE[] (MESA, PIVUS), or MACH[] (ARIC, GOLDN, HPFS, NHS). Compared to 1000G imputation, HapMap imputation allows similar identification of common variants when usi […]


Deep whole genome sequencing reveals recent selection signatures linked to evolution and disease risk of Japanese

Nat Commun
PMCID: 5915442
PMID: 29691385
DOI: 10.1038/s41467-018-03274-0

[…] quality score recalibration was applied according to the GATK Best Practice recommendations. We removed the variants located in the low complexity regions, and genotype refinement was performed using Beagle (versions 3.3.2 for the dataset 1, and version 4.1 for the datasets 2 and 3). We excluded the subjects with excess genotype heterozygosity, or excess numbers of singletons. Finally, we applied […]


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
call_split See protocol

[…] 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

Front Genet
PMCID: 5900008
PMID: 29686696
DOI: 10.3389/fgene.2018.00119
call_split See protocol

[…] 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. And then […]


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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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