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 vcf file named imputed_file. Is there anything missing in my script? I got to know that "ref=' argument which refers to reference data is required to get imputation accuracy metrics, AR2 or DR2. Can I get the reference data from the VCF file I am working on? If not where do I source reference data from?
My script for the imputation is as follows:
java -Xmx10g -jar /programs/beagle/beagle.jar gt=snps_filtered.recode.vcf nthreads=10 iterations=12 out=imputed_file