diff --git a/perl/1kgScripts/runCallingPipeline.pl b/perl/1kgScripts/runCallingPipeline.pl
index 780c4993d..b26927e49 100755
--- a/perl/1kgScripts/runCallingPipeline.pl
+++ b/perl/1kgScripts/runCallingPipeline.pl
@@ -41,7 +41,7 @@ my $bsub = "bsub -q $queue -o $indelsHigh.sdout";
 if ($wait) {
     $bsub .= " -w \"ended($wait)\"";
 }
-my $command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -minConsensusFraction 0.5 -minCnt 2 -1kg -minFraction 0.".$indelFractionMultiplier."3 -o $indelsHigh";
+my $command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -minConsensusFraction 0.5 -minCnt 2 -1kg -minFraction 0.".$indelFractionMultiplier."3 -O $indelsHigh";
 execute("$bsub $command", $dry);
 
 my $indelsLow = "$outputHead.indels.low.calls";
@@ -49,7 +49,7 @@ $bsub = "bsub -q $queue -o $indelsLow.sdout -J $outputHead";
 if ($wait) {
     $bsub .= " -w \"ended($wait)\"";
 }
-$command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -minConsensusFraction 0.5 -minCnt 2 -1kg -minFraction 0.".$indelFractionMultiplier."1 -o $indelsLow";
+$command = "java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -minConsensusFraction 0.5 -minCnt 2 -1kg -minFraction 0.".$indelFractionMultiplier."1 -O $indelsLow";
 execute("$bsub $command", $dry);
 
 if ($snps) {
diff --git a/perl/1kgScripts/runCleaningPipeline.pl b/perl/1kgScripts/runCleaningPipeline.pl
index 425a61f37..6025fa1cc 100755
--- a/perl/1kgScripts/runCleaningPipeline.pl
+++ b/perl/1kgScripts/runCleaningPipeline.pl
@@ -65,7 +65,7 @@ if ($inject) {
 }
 $command = "bsub -q $queue -o $outputBam.cleaner.script1 -w \"ended($outputBam.merged)\" -J $outputBam.cleaner.script perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -compress 1";
 if ($inject) {
-    $command .= " -cleanedOnly\" -j $outputBam.cleaned";
+    $command .= " -cleanedOnly\" -j $outputBam.cleaner.clean";
 } else {
     $command .= "\" -j $jobName";
 }
@@ -83,7 +83,7 @@ if (!$snpsFile) {
 }
 $command = "bsub -q $queue -o $outputBam.cleaner.script2 -w \"ended($outputBam.merged)\" -J $outputBam.cleaner.script perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\"";
 if ($inject) {
-    $command .= " -j $outputBam.cleaned";
+    $command .= " -j $outputBam.cleaner.badsnps";
 } else {
     $command .= " -j $jobName";
 }
@@ -101,7 +101,7 @@ if ($inject) {
     if ($jobName) {
 	$command .= " -J $jobName";
     }
-    $command .= " -w \"ended($outputBam.cleaned)\" java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T CleanedReadInjector -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam --output_bam $bam --cleaned_reads $cleanedBam -compress 1";
+    $command .= " -w \"ended($outputBam.cleaner.*)\" java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T CleanedReadInjector -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam --output_bam $bam --cleaned_reads $cleanedBam -compress 1";
     if ($dry) {
 	print "$command\n";
     } else {
diff --git a/perl/1kgScripts/runPilot1Pipeline.pl b/perl/1kgScripts/runPilot1Pipeline.pl
index a73dc6a1e..4a3b0ab81 100755
--- a/perl/1kgScripts/runPilot1Pipeline.pl
+++ b/perl/1kgScripts/runPilot1Pipeline.pl
@@ -31,7 +31,7 @@ foreach my $sample (@samples) {
     my $outputBam = "$outputHead.bam";
     my $badsnps = "$outputBam.badsnps";
     clean($inputBam, $outputBam, $queue, $sting, $dry, $badsnps);
-    call("-I $outputBam", $outputHead, $queue, $sting, $dry, "$inputBam.cleaningpipeline", $sample, $badsnps);
+    call("-I $outputBam", $outputHead, $queue, $sting, $dry, "$inputBam.cleaner.*", $sample, $badsnps);
 }
 
 sub clean {
@@ -43,7 +43,7 @@ sub clean {
     my $dry = $_[4];
     my $badsnps = $_[5];
 
-    my $cmd = "perl $sting/perl/1kgScripts/runCleaningPipeline.pl -i $inputBam -obam $outputBam -q $queue -j $outputBam.cleaningpipeline -sting $sting -badsnps $badsnps";
+    my $cmd = "perl $sting/perl/1kgScripts/runCleaningPipeline.pl -i $inputBam -obam $outputBam -q $queue -j $outputBam.cleaner.pipeline -sting $sting -badsnps $badsnps";
     if ($dry) {
 	$cmd .= " -dry";
     }
diff --git a/perl/1kgScripts/runPilot2Pipeline.pl b/perl/1kgScripts/runPilot2Pipeline.pl
index 22dab9568..91245ca8c 100755
--- a/perl/1kgScripts/runPilot2Pipeline.pl
+++ b/perl/1kgScripts/runPilot2Pipeline.pl
@@ -46,7 +46,7 @@ foreach my $sample (@samples) {
     my $outputBamSLX = "$outputHeadSLX.bam";
     my $badsnpsSLX = "$outputBamSLX.badsnps";
     clean($inputBamSLX, $outputBamSLX, $queue, $sting, $dry, $badsnpsSLX);
-    call("-I $outputBamSLX", $outputHeadSLX, $queue, $sting, $dry, "$inputBamSLX.cleaningpipeline", $sample, $badsnpsSLX, $DoC_slx{$sample}, $MQ_hash{"SLX"});
+    call("-I $outputBamSLX", $outputHeadSLX, $queue, $sting, $dry, "$outputBamSLX.cleaner.*", $sample, $badsnpsSLX, $DoC_slx{$sample}, $MQ_hash{"SLX"});
 
     if ($sample eq "NA12878" || $sample eq "NA19240") {
 	my $inputBamSOLID = "$inputDir/$sample.pilot2.SOLID.bam";
@@ -54,17 +54,17 @@ foreach my $sample (@samples) {
 	my $outputBamSOLID = "$outputHeadSOLID.bam";
 	my $badsnpsSOLID = "$outputBamSOLID.badsnps";
 	clean($inputBamSOLID, $outputBamSOLID, $queue, $sting, $dry, $badsnpsSOLID);
-	call("-I $outputBamSOLID", $outputHeadSOLID, $queue, $sting, $dry, "$inputBamSOLID.cleaningpipeline", $sample, $badsnpsSOLID, $DoC_solid{$sample}, $MQ_hash{"SOLID"});
+	call("-I $outputBamSOLID", $outputHeadSOLID, $queue, $sting, $dry, "$outputBamSOLID.cleaner.*", $sample, $badsnpsSOLID, $DoC_solid{$sample}, $MQ_hash{"SOLID"});
 
 	my $inputBam454 = "$inputDir/$sample.pilot2.454.bam";
 	my $outputHead454 = "$outputDir/$sample.454";
 	call("-I $inputBam454", $outputHead454, $queue, $sting, $dry, undef, $sample, $badsnpsSLX, $DoC_454{$sample}, $MQ_hash{"454"});
 
 	my $outputHead = "$outputDir/$sample.SOLID_454";
-	call("-I $outputBamSOLID -I $inputBam454", $outputHead, $queue, $sting, $dry, "$inputBamSOLID.cleaningpipeline", $sample, $badsnpsSOLID, $DoC_454solid{$sample}, $MQ_hash{"454SOLID"});
+	call("-I $outputBamSOLID -I $inputBam454", $outputHead, $queue, $sting, $dry, "$outputBamSOLID.cleaner.*", $sample, $badsnpsSOLID, $DoC_454solid{$sample}, $MQ_hash{"454SOLID"});
 
 	$outputHead = "$outputDir/$sample.allTechs";
-	call("-I $outputBamSLX -I $outputBamSOLID -I $inputBam454", $outputHead, $queue, $sting, $dry, "*.cleaningpipeline", $sample, $badsnpsSLX, $DoC_all{$sample}, $MQ_hash{"ALL"});
+	call("-I $outputBamSLX -I $outputBamSOLID -I $inputBam454", $outputHead, $queue, $sting, $dry, "*.cleaner.*", $sample, $badsnpsSLX, $DoC_all{$sample}, $MQ_hash{"ALL"});
     }
 }
 
@@ -77,7 +77,7 @@ sub clean {
     my $dry = $_[4];
     my $badsnps = $_[5];
 
-    my $cmd = "perl $sting/perl/1kgScripts/runCleaningPipeline.pl -i $inputBam -obam $outputBam -q $queue -inject -j $outputBam.cleaningpipeline -sting $sting -badsnps $badsnps";
+    my $cmd = "perl $sting/perl/1kgScripts/runCleaningPipeline.pl -i $inputBam -obam $outputBam -q $queue -inject -j $outputBam.cleaner.pipeline -sting $sting -badsnps $badsnps";
     if ($dry) {
 	$cmd .= " -dry";
     }
diff --git a/perl/splitAndEnqueueGATKjobs.pl b/perl/splitAndEnqueueGATKjobs.pl
index 388c6fed7..20641c0a7 100755
--- a/perl/splitAndEnqueueGATKjobs.pl
+++ b/perl/splitAndEnqueueGATKjobs.pl
@@ -128,11 +128,11 @@ sub mergeResults {
 	    $cmd .= "$output.$i.bam ";
 	}
     } else {
-	$cmd .= " cat ";
+	$cmd .= " \"cat ";
 	for (my $i = 1; $i <= $intervalcount; $i++) {
 	    $cmd .= "$output.$i ";
 	}
-	$cmd .= "> $output";
+	$cmd .= "> $output\"";
     }
 
     execute($cmd, $dry);