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• 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?
• Minimum # markers per chromosome/scaffold for imputation with Beagle 5.1
  I have a multisample vcf file from a study species with a pretty fragmented reference genome. I a...
• Recs for what to use for analyzing IBS sharing (from phased, imputed VCFs)?
  I have imputed GZ.VCFs from Beagle 4.0 based on some ancient DNA VCFs (24 individuals). Beagle ph...
• General approach for genotype refinement after GATK processing?
  Hi guys, Very new to all this so please bare with me. I just finished running through GATK's be...
• 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...
• 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...
• Creating Reference Set for Beagle Imputation
  Hello, I am looking to create a reference set of samples based off of their relatedness. I need ...
• Pre-phasing for imputation BEAGLE or MACH
  Hello, I'm performing pre-phasing for imputation in MACH. However, this is very time consuming. ...
• Running Beagle for imputation
  Hello, i work on a Macbook Pro with 16Go and i want to run Beagle using this syntax: java ...
• Convert beagle output file to plink
  I have a imputed beagle file. Is there a way so that we can we read it back in plink ?
• Haplotype phasing and imputation in Beagle 5.1
  Dear members, Anybody elaborate on the steps for **haplotype phasing and imputation in Beagle v5....
• How to determine the haplotypes using Beagle
  I have two datasets one has genotype data for 30 SNPs and one has genotype data for 29 SNPs.I wan...
• Imputation of vcf file
  Hi everyone, I have vcf file in dosage format like 0/0, 0/1 and etc. After filtering for quality,...
• Beagle imputation run time
  Hello, I am running beagle5.1 and am wondering about runtime and input limits. I have successful...
• Apply beagle5.0 to make imputation and phasing under CentOS and PBS
  I didn't find beagle imputation and phasing tutorial, therefore, try to give one sine I am using ...
• 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...
• Imputing phased beagle files using minimac
  Hello ! I have a multi-sample vcf that was phased using beagle. This serves as my reference. For...
• Beagle imputation results quality control
  My region of interest is ~ 120 kb. I have 300 samples, all containing 14 SNPs in the region. I tr...