Question: how to obtain imputation accuracy - allelic R2 in beagle
gravatar for mab658
21 months ago by
mab65880 wrote:

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
beagle snp • 1000 views
ADD COMMENTlink modified 21 months ago by zx875410.0k • written 21 months ago by mab65880
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1773 users visited in the last hour