diff --git a/src/ChrCopyNumber.cpp b/src/ChrCopyNumber.cpp
index ca5564a..b9d01c8 100644
--- a/src/ChrCopyNumber.cpp
+++ b/src/ChrCopyNumber.cpp
@@ -640,6 +640,11 @@ void ChrCopyNumber::calculateRatio(double *a, int degree) {
 //	}
 //}
 
+bool ChrCopyNumber::ifHasRatio() {
+    if (ratio_.size()>0) return 1;
+    return 0;
+}
+
 void ChrCopyNumber::recalculateRatio (float constant) {
 	for (int i = 0; i<length_; i++)
 		if (ratio_[i] != NA)
@@ -1684,9 +1689,11 @@ void ChrCopyNumber::addBAFinfo(SNPinGenome & snpingenome,int indexSNP) {
             }
         }
     }
-
+    if (ratio_.size()==0) {
+        cerr << "Warning: Normalized read counts (ratio_) has not been initialized; check your parameters\n";
+    }
     for (int i = 0; i<length_; i++) {
-        if (ratio_[i]==NA && BAF_[i]!=NA)     //set BAF=NA in windows with ratio==NA to remove the noise from windows with low mappability
+        if (ratio_.size()>i && ratio_[i]==NA && BAF_[i]!=NA)     //set BAF=NA in windows with ratio==NA to remove the noise from windows with low mappability
             BAF_[i]=NA;
 
         if (BAF_[i]==0)     //remove windows with 100% AA counts
diff --git a/src/ChrCopyNumber.h b/src/ChrCopyNumber.h
index bc6f119..13e1833 100644
--- a/src/ChrCopyNumber.h
+++ b/src/ChrCopyNumber.h
@@ -98,7 +98,7 @@ class ChrCopyNumber
 
 	bool isMedianCalculated();
 	bool isSmoothed();
-
+    bool ifHasRatio();
 
 
 	void fillCGprofile(std::string const& chrFolder);
diff --git a/src/GenomeCopyNumber.cpp b/src/GenomeCopyNumber.cpp
index adce9d1..3800f42 100644
--- a/src/GenomeCopyNumber.cpp
+++ b/src/GenomeCopyNumber.cpp
@@ -1099,6 +1099,11 @@ int GenomeCopyNumber::getNumberOfChromosomes() {
     return chrCopyNumber_.size();
 }
 
+bool GenomeCopyNumber::ifHasRatio() {
+    if (chrCopyNumber_[0].ifHasRatio()) return 1;
+    return 0;
+}
+
 long double GenomeCopyNumber::calculateRSS(int ploidy)
 {
     string::size_type pos = 0;
diff --git a/src/GenomeCopyNumber.h b/src/GenomeCopyNumber.h
index 98fe751..6770891 100644
--- a/src/GenomeCopyNumber.h
+++ b/src/GenomeCopyNumber.h
@@ -110,6 +110,7 @@ class GenomeCopyNumber
     bool getWESanalysis();
     double getGenomeRefSize();
     int getNumberOfChromosomes();
+    bool ifHasRatio();
 
 
 	void setPloidy(int ploidy);
diff --git a/src/SNPinGenome.cpp b/src/SNPinGenome.cpp
index 3c5f96a..9119272 100644
--- a/src/SNPinGenome.cpp
+++ b/src/SNPinGenome.cpp
@@ -213,18 +213,23 @@ void SNPinGenome::perform(std::string const& mateFile, const std::string& inputF
     if (!pileup_read) {
 	  assignValues(mateFile, inputFormat, minimalTotalLetterCountPerPosition,minimalQualityPerPosition);
 	}
-	cout << "..Adding BAF info to the " << what << " dataset" << std::endl;
-	genomeCopyNumber.addBAFinfo(*this);
-	cout << "..Recalculate breakpoints using BAF profiles" << std::endl;
-	genomeCopyNumber.calculateBAFBreakpoints(breakPointThreshold,breakPointType);
-	cout << "..Recalculate median values" << std::endl;
-	genomeCopyNumber.calculateCopyNumberMedians(minCNAlength, noisyData, CompleteGenomicsData);
-
-	cout << "..Reannotate copy numbers" << std::endl;
-	if (genomeCopyNumber.getWESanalysis() == false)
-        {genomeCopyNumber.calculateCopyNumberProbs_and_genomeLength(breakPointType);}
-    else
-        {genomeCopyNumber.calculateCopyNumberProbs_and_exomeLength(breakPointType);}
+
+	if (genomeCopyNumber.ifHasRatio()) {
+        cout << "..Adding BAF info to the " << what << " dataset" << std::endl;
+        genomeCopyNumber.addBAFinfo(*this);
+        cout << "..Recalculate breakpoints using BAF profiles" << std::endl;
+        genomeCopyNumber.calculateBAFBreakpoints(breakPointThreshold,breakPointType);
+        cout << "..Recalculate median values" << std::endl;
+        genomeCopyNumber.calculateCopyNumberMedians(minCNAlength, noisyData, CompleteGenomicsData);
+
+        cout << "..Reannotate copy numbers" << std::endl;
+        if (genomeCopyNumber.getWESanalysis() == false)
+            {genomeCopyNumber.calculateCopyNumberProbs_and_genomeLength(breakPointType);}
+        else
+            {genomeCopyNumber.calculateCopyNumberProbs_and_exomeLength(breakPointType);}
+
+    }
+
 	cout << "..Done" << std::endl;
 }
 
diff --git a/src/freec b/src/freec
index 097c42b..9885bd8 100644
Binary files a/src/freec and b/src/freec differ
diff --git a/src/main.cpp b/src/main.cpp
index 9d57748..4424d66 100644
--- a/src/main.cpp
+++ b/src/main.cpp
@@ -707,8 +707,8 @@ int main(int argc, char *argv[])
 	snpingenome.setWESanalysis(WESanalysis);
 	SNPinGenome snpingenomeControl;
     snpingenomeControl.setWESanalysis(WESanalysis);
-    if (makePileup== "false") {
-        snpingenome.setCopyNumberFromPileup(true); //use pileup for copy number asessment, not only for BAFs
+    if (makePileup== "false" && !isHasMiniPileUPcontrol && !isHasMiniPileUPsample) {
+        snpingenome.setCopyNumberFromPileup(true); //use pileup for copy number assessment, not only for BAFs
         snpingenomeControl.setCopyNumberFromPileup(true);
     }
 
@@ -1070,7 +1070,7 @@ int main(int argc, char *argv[])
 
 	    sampleCopyNumber.printBAF(myName,snpingenome,sample_MateFile);
 
-        if (isControlIsPresent && makePileup == "false") {
+        if (isControlIsPresent && makePileup == "false" && !ifTargeted) { // will output Control data only for WGS data!
             sampleCopyNumber.calculateSomaticCNVs(controlCopyNumber.getCNVs(),controlCopyNumber.getPloidy());
             controlCopyNumber.printBAF(controlName,snpingenomeControl,control_MateFile);
             controlCopyNumber.printRatio(myName+"_normal_ratio.txt",0,printNA);
diff --git a/src/version.h b/src/version.h
index f3d2f98..4135a6d 100644
--- a/src/version.h
+++ b/src/version.h
@@ -3,7 +3,7 @@
 #define VERSION_H
 
 const double VERSION_OFFSET = 3;
-const double FREEC_VERSION = 11.3;
+const double FREEC_VERSION = 11.4;
 const double CONTROL_FREEC_VERSION = FREEC_VERSION - VERSION_OFFSET;
 
 #endif