--- a/libexec/consolidateResults.pl	Fri Sep 26 14:33:07 2014 +0200
+++ b/libexec/consolidateResults.pl	Fri Sep 26 15:51:35 2014 +0200
@@ -35,24 +35,18 @@
 
 my $baseDir;
 my $libDir;
-#my $optDir;
-#my $vcftDir;
 BEGIN {
     my $thisDir=(File::Spec->splitpath($0))[1];
     $baseDir=File::Spec->catdir($thisDir,File::Spec->updir());
     $libDir=File::Spec->catdir($baseDir,'lib');
-    #$optDir=File::Spec->catdir($baseDir,'opt');
-    #$vcftDir=File::Spec->catdir($optDir,'vcftools','lib','perl5','site_perl');
 }
 use lib $libDir;
 use Utils;
-#use lib $vcftDir;
 use Vcf;
 
 if(getAbsPath($baseDir)) {
     errorX("Can't resolve path for strelka_workflow install directory: '$baseDir'");
 }
-#$optDir=File::Spec->catdir($baseDir,'opt');
 
 
 my $scriptName=(File::Spec->splitpath($0))[2];
@@ -70,13 +64,6 @@
 pod2usage(2) unless(defined($configFile));
 
 #
-# check fixed paths
-#
-#my $samtoolsBin = File::Spec->catfile($optDir,'samtools','samtools');
-#checkFile($samtoolsBin,"samtools binary");
-
-
-#
 # read config and validate values
 #
 checkFile($configFile,"configuration ini");
@@ -247,17 +234,17 @@
     return unless(scalar(@bamList));
 
     my $headerFH = File::Temp->new();
-    my $getHeaderCmd = "bash -c '$samtoolsBin view -H ".$bamList[0]." > $headerFH'";
+    my $getHeaderCmd = "bash -c 'samtools view -H ".$bamList[0]." > $headerFH'";
     executeCmd($getHeaderCmd);
 
     my $allFile = File::Spec->catfile($reDir,$fileName . $itag);
-    my $cmd="$samtoolsBin merge -h $headerFH $allFile ". join(" ",@bamList);
+    my $cmd="samtools merge -h $headerFH $allFile ". join(" ",@bamList);
     executeCmd($cmd);
 
     my $allFileFinished = File::Spec->catfile($reDir,$fileName);
     checkMove($allFile,$allFileFinished);
 
-    my $indexCmd="$samtoolsBin index $allFileFinished";
+    my $indexCmd="samtools index $allFileFinished";
     executeCmd($indexCmd);
 
     # for now don't remove all the bin realignments...