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• Beagle: Skip intervals with no common markers
  Hi I am using Beagle to perform genotype imputation. I first used conform-gt to adjust genomic p...
• How to run Beagle to impute missing data using reference panel (1000 genome)?
  Hi, I'm a real beginner with beagle and i want to know how to impute on Beagle 4.1 my missing da...
• check the accurancy of the imputation using beagle 4.1
  Hello, to check if beagle does the imputation well, After imputing my data with Beagle 4.1, I wi...
• Phasing vcf file with Beagle
  Hello all, I tried to phase my vcf files with Beagle. All the genotypes seem to be phased but t...
• How to impute missing SNPs of genotypic data of plant species, without having HapMap reference panel?
  hello all, I have a SNP genotype data of 228 accessions of cotton, on which I want to do GWAS. T...
• how to obtain imputation accuracy - allelic R2 in beagle
  Dear All, I used beagle for imputation but I could not see the allelic Rsquare (AR2) which measur...
• How I can imputed low density (5k) to 50K by beagle software?
  I want use Beagle to impute my data; How I can imputed low density (5k) to 50K by beagle software?
• How does beagle get phase for sites that are NOT in the reference panel
  Im doing some phasing and genotype imputation of a target data set using a reference panel and Be...
• Phasing genotype per chromosomes in Beagle software
    I want to use beagle to phase my genotyped per chromosome, my data is in AB, format. When I ru...
• Running Beagle for imputation
  Hello, i work on a Macbook Pro with 16Go and i want to run Beagle using this syntax: java ...
• Beagle phasing without map and reference parameters
  Hi All, I just find beagle can do the phasing without map and reference parameters. Anyone can ...
• How is genotype imputation used in variant calling pipelines
  In the [supplementary][1] of phase 1 1000 genomes they say: > "The merged genotype likelihood...
• Beagle Imputation Markers List
  Hi, I 'm trying to impute genotype calls using Beagle and reference panel. I have a likelihood fi...
• Interpreting phased data from Beagle
  Dear all, I'm trying to investigate how Beagle works when phasing with a reference panel and wit...
• Beagle 4.1 imputation
  I am running Beagle 4.1 to impute SNPs in human WGS data. I ran chr 21 and it took 10 days. (wi...
• Genotype Phasing When Using The Beagle Genetic Analysis Software
  Hello, can somebody who knows BEAGLE a bit tell me whether you are supposed to phase your sample...
• Imputation without reference for small number of samples/taking care of missing values
  Hi all, I am trying to do some association study using SNPs called from RNA-seq experiment. My s...
• Imputation Without A Reference Panel
  I would like to know if there are there any tools to impute missing SNPs for a resequencing datas...
• beagle 4 exception: Duplicate marker
  I'm trying to use BEAGLE 4 to do an IBD analysis. I'm running the command: java -jar beagle.r139...
• Imputing missing genotypes using Beagle
  Hi! I want to use Beagle version 5.1. to exclusively impute my missing genotypes (no ref. panel n...