diff --git a/perl/1kgScripts/runCleaningPipeline.pl b/perl/1kgScripts/runCleaningPipeline.pl
index 4b8b5f80d..425a61f37 100755
--- a/perl/1kgScripts/runCleaningPipeline.pl
+++ b/perl/1kgScripts/runCleaningPipeline.pl
@@ -63,33 +63,37 @@ if ($inject) {
 } else {
     $cleanedBam = "$outputBam";
 }
-$command = "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 $inputBam -compress 1";
+$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";
 } else {
     $command .= "\" -j $jobName";
 }
-$command .= " -o $cleanedBam -oarg O -wait $outputBam.merged -q $queue -bam -i $mergedIntervals -n 50";
+$command .= " -o $cleanedBam -oarg O -q $queue -bam -i $mergedIntervals -n 50";
 if ($dry) {
     $command .= " -dry";
+    print "$command\n";
+} else {
+    system($command);
 }
-system($command);
 
 my $snpsFile = $badsnps;
 if (!$snpsFile) {
     $snpsFile = "$outputBam.badsnps";
 }
-$command = "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 $inputBam\"";
+$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";
 } else {
     $command .= " -j $jobName";
 }
-$command .= "\" -o $snpsFile -oarg snps -wait $outputBam.merged -q $queue -i $mergedIntervals -n 50";
+$command .= " -o $snpsFile -oarg snps -q $queue -i $mergedIntervals -n 50";
 if ($dry) {
     $command .= " -dry";
+    print "$command\n";
+} else {
+    system($command);
 }
-system($command);
 
 if ($inject) {
     my $bam = "$outputBam";
diff --git a/perl/1kgScripts/runPilot2Pipeline.pl b/perl/1kgScripts/runPilot2Pipeline.pl
index 92f5da232..b1f5cebdc 100755
--- a/perl/1kgScripts/runPilot2Pipeline.pl
+++ b/perl/1kgScripts/runPilot2Pipeline.pl
@@ -15,7 +15,7 @@ my $queue = "gsa";
 my $sting = "/humgen/gsa-scr1/ebanks/Sting";
 
 GetOptions( "i=s" => \$inputDir,
-	    "odir=s" => \$outputDir,
+	    "o=s" => \$outputDir,
 	    "q:s" => \$queue,
 	    "dry!" => \$dry,
 	    "sting:s" => \$sting );
@@ -44,7 +44,7 @@ foreach my $sample (@samples) {
     my $inputBamSLX = "$inputDir/$sample.pilot2.SLX.bam";
     my $outputHeadSLX = "$outputDir/$sample.SLX";
     my $outputBamSLX = "$outputHeadSLX.bam";
-    my $badsnpsSLX = "$outputDir/$outputBamSLX.badsnps";
+    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"});
 
@@ -52,7 +52,7 @@ foreach my $sample (@samples) {
 	my $inputBamSOLID = "$inputDir/$sample.pilot2.SOLID.bam";
 	my $outputHeadSOLID = "$outputDir/$sample.SOLID";
 	my $outputBamSOLID = "$outputHeadSOLID.bam";
-	my $badsnpsSOLID = "$outputDir/$outputBamSOLID.badsnps";
+	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"});
 
diff --git a/perl/1kgScripts/runPilotPipelines.sh b/perl/1kgScripts/runPilotPipelines.sh
index 3c3230815..d95c9634b 100755
--- a/perl/1kgScripts/runPilotPipelines.sh
+++ b/perl/1kgScripts/runPilotPipelines.sh
@@ -1,2 +1,2 @@
-#perl /humgen/gsa-scr1/ebanks/Sting/perl/1kgScripts/runPilot1Pipeline.pl -i /humgen/gsa-hphome1/projects/1kg_pilot1/mergedBamsByPopulation -o /broad/hptmp/ebanks/1kg_pilot1/cleaned -dry
-perl /humgen/gsa-scr1/ebanks/Sting/perl/1kgScripts/runPilot2Pipeline.pl -i /broad/1KG/DCC_merged/freeze5.2 -o /broad/hptmp/ebanks/1kg_pilot2/cleaned -dry
+#perl /humgen/gsa-scr1/ebanks/Sting_STABLE/perl/1kgScripts/runPilot1Pipeline.pl -i /humgen/gsa-hphome1/projects/1kg_pilot1/mergedBamsByPopulation -o /broad/hptmp/ebanks/1kg_pilot1/cleaned -sting /humgen/gsa-scr1/ebanks/Sting_STABLE -dry 
+perl /humgen/gsa-scr1/ebanks/Sting_STABLE/perl/1kgScripts/runPilot2Pipeline.pl -i /broad/1KG/DCC_merged/freeze5.2 -o /broad/hptmp/ebanks/1kg_pilot2/cleaned -sting /humgen/gsa-scr1/ebanks/Sting_STABLE