“…Here, we investigated the imputation performance of three representative versions of Beagle (Beagle 4.1, Beagle 5.0, and Beagle 5.4), and the effective population size (Ne) parameter setting for three species (cattle, pig, and chicken). …”
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“…When Beagle was used alone, the imputation error rate was 0.67%. …”
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“…In this study, we compared the efficiency of three widely used imputation algorithms (fastPHASE, BEAGLE and findhap) using Chinese Holstein cattle with Illumina BovineSNP50 genotypes. …”
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“…FImpute haplotypes showed a higher number of Bkp than Beagle. As a consequence, switched haplotype segments were longer for Beagle than for FImpute. …”
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“…BACKGROUND: Neonatal cerebellar cortical degeneration is a neurodegenerative disease described in several canine breeds including the Beagle. Affected Beagles are unable to ambulate normally from the onset of walking and the main pathological findings include Purkinje cell loss with swollen dendritic processes. …”
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“…Here we investigated the pathogenicity of different infectious doses of H3N2 CIV in Beagle dogs. Thirty-seven healthy Beagle dogs were used in the experiment and were infected with 10(3), 10(4), 10(5), and 10(6) 50% egg-infectious doses (EID(50)). …”
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“…For fast and accurate imputation, a combination of Eagle2.4.1 using a reference panel for phasing and Beagle5.1 for imputation performs best. Replacing Beagle5.1 with minimac3, minimac4, Beagle4.1, or IMPUTE4 results in a small gain in accuracy at a high cost of speed.…”
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“…The simulation studies showed that the algorithm exhibited drastically tolerance to high missing rate, especially for rare variants than other common imputation methods, e.g. BEAGLE and fastPHASE. At a missing rate of 70%, the accuracy of BEAGLE and fastPHASE dropped to 0.82 and 0.74 respectively while iBLUP retained an accuracy of 0.95. …”
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“…Pre-phasing the reference data only lead to a minor decrease in the imputation accuracy, but gave a large improvement in computation time. Pre-phasing with BEAGLE was substantially faster than pre-phasing with SHAPEIT2 (2.5 hours vs. 52 hours for 242 individuals), and imputation with pre-phased data was faster in IMPUTE2 than in BEAGLE (5 minutes vs. 50 minutes per individual). …”
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“…Accuracy of imputation from putative 60 K and 600 K array data to WGS data was 0.620 and 0.812 for Beagle, and 0.810 and 0.914 for FImpute, respectively. …”
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“…The accuracy of state-of-the-art, LD-based imputation methods (IMPUTE, Beagle) was assessed by measuring allelic r(2) for 459 P. falciparum samples from malaria patients in 4 countries: Thailand, Cambodia, Gambia, and Malawi. …”
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“…In this study, we compared the latest versions of the most popular HMM-based tools for phasing and imputation: Beagle5.4, Eagle2.4.1, Shapeit4, Impute5 and Minimac4. …”
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“…We also observed that a greater number of haplotypes in the reference sample resulted in higher ARs for MACH, IMPUTE, PLINK and Beagle, but had little influence on the ARs for fastPHASE. …”
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“…RESULTS: The average concordance rate using FImpute was 0.943 and 0.921 averaged across all simulated low density panels to 50K or to 777K, respectively, in comparison with 0.927 and 0.895 using Beagle. The allelic R(2) was 0.912 and 0.866 for imputation to 50K or to 777K using FImpute, respectively, and 0.890 and 0.826 using Beagle. …”
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“…RESULTS: For the DL-line (LW-line), imputation of 80 K genotypes to iWGS resulted in an average Beagle R(2) of 0.39 (0.49). After quality control, 2.5 × 10(6) (3.5 × 10(6)) SNPs had a Beagle R(2) higher than 0.6, resulting in an average Beagle R(2) of 0.83 (0.93). …”
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“…The use of this method was exemplified in pharmacokinetic study of beagle dog plasma after oral administration of PNS. …”
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“…FImpute had higher imputation accuracy (93.94%) than Findhap (84.64%) and Beagle (76.79%). Imputation accuracies were similar and consistent across chromosomes for FImpute, but not for Findhap and Beagle. …”
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“…A semi-mechanistic pharmacokinetic/pharmacodynamic (PK/PD) model was developed to characterize the PK of HY-021068 and its platelet aggregation inhibitory effect in beagle dogs. Method: Beagle dogs received single oral administration of 2.5 mg/kg HY-021068 or consecutively oral administration of 5 mg/kg HY-021068 once daily for 7 days. …”
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“…The plasma protein binding degree of BZP at three concentrations (8000, 20,000, and 80,000 ng/mL) from rat, beagle dog, and human plasma were 98.1–98.7, 88.9–92.7, and 74.8–83.7% respectively. …”
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“…RESULTS: Four MAFs (no MAF limit, MAF ≥ 0.001, MAF ≥ 0.01 and MAF ≥ 0.03) were used for editing marker data before imputation. Beagle, IMPUTE2 and FImpute software were applied to impute the original GBS. …”
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