BEAGLE statistics

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Citations per year

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Popular tool citations

chevron_left Genotype imputation Haplotype phasing chevron_right
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Tool usage distribution map

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Associated diseases

Associated diseases


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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



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  • person_outline Brian L. Browning <>

Publications for BEAGLE

BEAGLE in pipelines

PMCID: 5461113
PMID: 28585919
DOI: 10.7554/eLife.22536.042

[…] clustered with the mexican american reference (mxl) population by multi-dimensional scaling analysis in plink (). snvs were then phased according to the 1000 genomes mxl reference population in beagle (; )., allele-specific binding of jun and nfκb/p65 was quantified using the wasp pipeline (). to avoid mapping bias caused by alternate alleles, reads that mapped discordantly to reference […]

PMCID: 5490002
PMID: 28643794
DOI: 10.1038/ncomms15927

[…] (a total of 9,375) was performed with the defined site selection criteria (). genotype likelihoods were calculated with samtools/bcftools (0.2.0-rc9) and then genotypes were called and phased using beagle v4 (r1274) (ref. ). we assessed the performance of the genotype calling from the low coverage data using the available genotype chip data for a subset of the cohorts consisting of 4,665 […]

PMCID: 5558724
PMID: 28810831
DOI: 10.1186/s12864-017-4030-x

[…] bulls, and 114 australian red bulls were genotyped with the 777 k bovine hd snp panel. after quality control steps described by erbe et al. (2012) [], all genotypes were imputed to 632,003 snp using beagle 3.0 []., for the sequence data set (termed seq), the sequences of 136 holstein and 27 jersey bulls from the 1000 bulls genome project [] were used as a reference set for imputation. […]

PMCID: 5680825
PMID: 29121877
DOI: 10.1186/s12864-017-4278-1

[…] additional file : table s3). inbreeding assessment was performed by calculating the f coefficient (observed vs expected homozygous genotype counts) in plink v1.90b3.30 []., we used the pedigree based beagle version 4.0 genetic analysis software for phasing and imputation of samples []. first, 10 k samples were imputed to 60 k per individual breeding line. this differs for the boar line in which we […]

PMCID: 5683586
PMID: 29132403
DOI: 10.1186/s13059-017-1346-4

[…] vcftools v.0.1.12 [] was used to further filter snps to include only bi-allelic sites. following these data filtering steps, our data set consisted of 49 million snps. snps were phased using beagle v.4.0 [] with snp data from the maize hapmap2 panel [] used as a reference. only sites with depth between half and twice of the mean depth were included in analyses. in addition, the software […]

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BEAGLE in publications

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 […]

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 […]

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 […]

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. […]

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 […]

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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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