Question: how to obtain imputation accuracy - allelic R2 in beagle
1
gravatar for mab658
18 months ago by
mab65880
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 • 840 views
ADD COMMENTlink modified 18 months ago by zx87549.7k • written 18 months ago by mab65880
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