BEAGLE protocols

BEAGLE specifications

Information


Unique identifier OMICS_00052
Name BEAGLE
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

Subtool


  • FastIBD

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Documentation


Maintainer


  • person_outline Brian L. Browning <>

Publications for BEAGLE

BEAGLE IN pipelines

 (37)
2017
PMCID: 5404774
PMID: 28441463
DOI: 10.1371/journal.pone.0175957

[…] frequent genotype based on the distribution of the snps genotypes (1, 2, or 3) across cases. for large numbers of missing genotypes, several established methods and tools, such as impute [60,61], beagle [62] and plink could be used., the pipeline is solely generic in use for the identification of key significant snps within candidate genes associated with continuous phenotypic traits. […]

2017
PMCID: 5461113
PMID: 28585919
DOI: 10.7554/eLife.22536.042

[…] the mexican american reference (mxl) population by multi-dimensional scaling analysis in plink (purcell et al., 2007). snvs were then phased according to the 1000 genomes mxl reference population in beagle (browning and browning, 2016; browning and browning, 2007)., allele-specific binding of jun and nfκb/p65 was quantified using the wasp pipeline (van de geijn et al., 2015). to avoid mapping […]

2017
PMCID: 5490002
PMID: 28643794
DOI: 10.1038/ncomms15927

[…] was performed with the defined site selection criteria (supplementary note). genotype likelihoods were calculated with samtools/bcftools (0.2.0-rc9) and then genotypes were called and phased using beagle v4 (r1274) (ref. 35). 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 […]

2017
PMCID: 5558724
PMID: 28810831
DOI: 10.1186/s12864-017-4030-x

[…] 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) [7], all genotypes were imputed to 632,003 snp using beagle 3.0 [17]., for the sequence data set (termed seq), the sequences of 136 holstein and 27 jersey bulls from the 1000 bulls genome project [1] were used as a reference set for imputation. […]

2017
PMCID: 5558724
PMID: 28810831
DOI: 10.1186/s12864-017-4030-x

[…] 1000 bulls genome project [1] were used as a reference set for imputation. all the animals described above with real or imputed 600 k snp genotypes were imputed to whole genome sequence data using beagle 3.0 software [18]. in total there were 2.785 million sequence variants imputed, including both snps and indels in either coding regions or putative regulatory regions flanking genes [5]. […]

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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