diff --git a/gwas/aou/README.md b/gwas/aou/README.md
index 0e339f52..78a2997e 100644
--- a/gwas/aou/README.md
+++ b/gwas/aou/README.md
@@ -54,6 +54,7 @@ Optional arguments:
 * `--MAF`: Apply minor allele frequency QC. Default=0.01
 * `--HWE`: Apply HWE p-value cutoff QC. Default=1e-15
 * `--GQ`: Apply minimun genotype score QC. Default=20
+* `--beagle-dosages`: Apply beagle dosages flag to associaTR. Default=false
 
 
 ## Important file locations:
diff --git a/gwas/aou/aou_gwas.py b/gwas/aou/aou_gwas.py
index 400a865d..8b4474b4 100755
--- a/gwas/aou/aou_gwas.py
+++ b/gwas/aou/aou_gwas.py
@@ -110,6 +110,7 @@ def main():
     parser.add_argument("--MAF", help="Apply minor allele frequency QC", type=float, default=0.01)
     parser.add_argument("--HWE", help="Apply HWE p-value cutoff QC", type=float, default=1e-100)
     parser.add_argument("--GQ", help="Apply minimun genotype score QC", type=int, default=20)
+    parser.add_argument("--beagle-dosages", help="Apply beagle dosages flag to associaTR ,Default: False",action="store_true")
     args = parser.parse_args()
 
     # Set up paths
@@ -185,7 +186,7 @@ def main():
         runner = HailRunner(data, region=args.region, covars=covars, sample_call_rate=args.sample_call_rate, variant_call_rate=args.variant_call_rate, MAF=args.MAF, HWE=args.HWE, GQ=args.GQ)
     elif args.method == "associaTR":
         from associatr_runner import AssociaTRRunner
-        runner = AssociaTRRunner(data, args.tr_vcf, region=args.region, covars=covars)
+        runner = AssociaTRRunner(data, args.tr_vcf, region=args.region, covars=covars, beagle=args.beagle_dosages)
     else:
         ERROR("GWAS method %s not implemented" % args.method)
 
diff --git a/gwas/aou/associatr_runner.py b/gwas/aou/associatr_runner.py
index a4524222..93f6fa0d 100644
--- a/gwas/aou/associatr_runner.py
+++ b/gwas/aou/associatr_runner.py
@@ -9,13 +9,14 @@
 import trtools.associaTR
 
 class AssociaTRRunner:
-    def __init__(self, ptcovar, trvcf, region=None, covars=[]):
+    def __init__(self, ptcovar, trvcf, beagle, region=None, covars=[]):
         self.ptcovar = ptcovar
         self.pt_npy = None
         self.covar_npy = None
         self.trvcf = trvcf
         self.region = region
         self.covars = covars
+        self.beagle = beagle
         self.gwas = None
         self.method = "associaTR"
         self.setup()
@@ -42,7 +43,7 @@ def RunGWAS(self):
         same_samples = False
         sample_list = None
         non_major_cutoff = 20
-        beagle_dosages = False
+        #beagle_dosages = False
         plotting_phenotype = None
         paired_genotype_plot = False
         plot_genotype_residuals = False
@@ -59,7 +60,7 @@ def RunGWAS(self):
             sample_list,
             self.region,
             non_major_cutoff,
-            beagle_dosages,
+            self.beagle,
             plotting_phenotype,
             paired_genotype_plot,
             plot_genotype_residuals,