diff --git a/R/logistic_regression.R b/R/logistic_regression.R
deleted file mode 100755
index 604323427..000000000
--- a/R/logistic_regression.R
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/broad/tools/apps/R-2.6.0/bin/Rscript
-
-args<- commandArgs(TRUE)
-verbose<- TRUE
-
-input_fileroot <- args[1]
-output_fileroot <- args[2]
-dinuc <- args[3]
-
-currentin=paste(input_fileroot,dinuc,"csv",sep=".");
-currentout=paste(output_fileroot,dinuc,"parameters",sep=".");
-con <- file(currentin, "r")
-con_out <- file(currentout, "w+")
-data<-read.table(con,header=TRUE,sep=",")
-reg<-glm(indicator~1+logitQ+I(logitQ^2)+I(logitQ^3)+I(logitQ^4)+pos+I(logitQ*pos)+I((logitQ^2)*pos)+I((logitQ^3)*pos)+I((logitQ^4)*pos)+I(pos^2)+I(logitQ*(pos^2))+I((logitQ^2)*(pos^2))+I((logitQ^3)*(pos^2))+I((logitQ^4)*(pos^2))+I(pos^3)+I(logitQ*(pos^3))+I((logitQ^2)*(pos^3))+I((logitQ^3)*(pos^3))+I((logitQ^4)*(pos^3))+I(pos^4)+I(logitQ*(pos^4))+I((logitQ^2)*(pos^4))+I((logitQ^3)*(pos^4))+I((logitQ^4)*(pos^4)),family=binomial("logit"),data=data, weights=data$count)
-write(coefficients(reg),file=con_out)
diff --git a/packages/GenomeAnalysisTK.xml b/packages/GenomeAnalysisTK.xml
index eeaad6a18..f93ba0680 100644
--- a/packages/GenomeAnalysisTK.xml
+++ b/packages/GenomeAnalysisTK.xml
@@ -51,11 +51,8 @@
     <file>testdata/exampleFASTA.fasta.fai</file>
     <file>testdata/exampleFASTA.dict</file>
     <!-- Supplemental scripts for graph generation, etc. -->
-    <file>python/analyzeRecalQuals.py</file>
     <file>python/analyzeRecalQuals_1KG.py</file>
-    <file>testdata/defaultGATKConfig.cfg</file>
     <file>testdata/recalConfig_1KG.cfg</file>
-    <file>R/logistic_regression.R</file>
     <file>R/plot_q_emp_stated_hst.R</file>
     <file>R/plot_qual_diff_v_cycle.R</file>
     <file>R/plot_qual_diff_v_dinuc.R</file>