--- a/admixture.sh	Tue Apr 12 09:31:56 2016 -0400
+++ b/admixture.sh	Wed Apr 13 07:51:13 2016 -0400
@@ -8,6 +8,8 @@
 best_k_logfile=$7
 kmin=$8
 kmax=$9
+groups=${10}
+threshold_group=${11}
 
 directory=`dirname $0`
 mkdir tmpdir$$
@@ -16,11 +18,12 @@
 cp -rf $bim tmpdir$$/input.bim
 
  
-perl $directory/Admixture.pl -i tmpdir$$/input -o $outputs -k $kmin -m $kmax -d tmpdir$$
+perl $directory/Admixture.pl -i tmpdir$$/input -o $outputs -k $kmin -m $kmax -d tmpdir$$ -t $threshold_group
 
 mv tmpdir$$/output $best_k_output
 mv tmpdir$$/log $best_k_logfile
 mv tmpdir$$/outputs.Q $outputs
 mv tmpdir$$/logs $logs
+mv tmpdir$$/groups $groups