Hi, I'm doing imputation using Beagle. I have a reference population which I use for imputing my target population. my reference population is a combination …

Hi there! I have just imputed some low-coverage (<4x) whole genome sequencing samples using a WGS reference panel (>10x) and Beagle v5.4: ``` java -jar …

Hi, I have a vcf file that has imputed markers after being phased through BEAGLE. I wanted to filter those SNPs and samples that have …

Hi all, I imputed a set of genotypes by beagle using the following function: java -jar beagle.jar gt=target.vcf ref=ref.vcf gp=true out=imputed With gp = true …

I had a vcf file with imputed genotypes from beagle like this: ##fileformat=VCFv4.2 ##filedate=20210504 ##source="beagle.18May20.d20.jar" ##INFO=<ID=AF,Number=A,Type=Float,Description="Estimated ALT Allele Frequencies"> ##INFO=<ID=DR2,Number=1,Type=Float,Description="Dosage R-Squared: estimated squared correlation between …

Hi, I have a multialleic record in VCF file: 1 15274 rs62636497 A G,T . PASS DR2=0.08,0.08;AF=0.454,0.5454;IMP GT:DS:AP1:AP2:GP 1|2:0.91,1.09:0.6,0.4:0.31,0.69:0,0,0.19,0,0.54,0.28 From the record I can see …

hello all, I have a SNP genotype data of 228 accessions of cotton, on which I want to do GWAS. The genotype data has a …

I'm working with imputed data in multisample bcf format which contains a FORMAT/GP field for each sample. I would like to set to missing (./.) …

Dear All, I used beagle for imputation but I could not see the allelic Rsquare (AR2) which measures the imputation accuracy in my new imputed …

Can anyone kindly explain me the possible ways of quality control of imputed data? Any reference papers or site describing post imputation quality control would …