diff --git a/perl/1kgScripts/runCleaningPipeline.pl b/perl/1kgScripts/runCleaningPipeline.pl
new file mode 100755
index 000000000..f38faf6a2
--- /dev/null
+++ b/perl/1kgScripts/runCleaningPipeline.pl
@@ -0,0 +1,91 @@
+#!/usr/bin/perl -w
+
+use strict;
+use Getopt::Long;
+
+sub usage {
+    print "Usage: perl runCleaningPipeline.pl\n\t-i <input bam>\n\t-odir <output directory>\n\t-obam <output bam name>\n\t[-sting Sting dir]\n\t[-inject]\n\t[-q farm queue; default:gsa]\n\t[-wait farm wait id]\n\t[-job final farm job name]\n\t[-dry]\n";
+    exit(1);
+}
+
+my $inputBam = undef;
+my $outputDir = undef;
+my $outputBam = undef;
+my $jobName = undef;
+my $wait = undef;
+my $dry;
+my $inject;
+my $queue = "gsa";
+my $sting = "/humgen/gsa-scr1/ebanks/Sting";
+
+GetOptions( "i=s" => \$inputBam,
+	    "odir=s" => \$outputDir,
+	    "obam=s" => \$outputBam,
+	    "q:s" => \$queue,
+	    "dry!" => \$dry,
+	    "inject!" => \$inject,
+	    "job:s" => \$jobName,
+	    "wait:s" => \$wait,
+	    "sting:s" => \$sting );
+
+usage() if ( !$inputBam || !$outputDir || !$outputBam );
+
+my $indelIntervals = "$outputDir/$outputBam.indels.intervals";
+my $command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\" -o $indelIntervals -oarg o -j $outputDir/$outputBam.intervals -q $queue";
+if ($dry) {
+    $command .= " -dry";
+}
+if ($wait) {
+    $command .= " -wait $wait";
+}
+system($command);
+
+my $mismatchIntervals = "$outputDir/$outputBam.mismatches.intervals";
+$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T MismatchIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\" -o $mismatchIntervals -oarg o -j $outputDir/$outputBam.intervals -q $queue";
+if ($dry) {
+    $command .= " -dry";
+}
+if ($wait) {
+    $command .= " -wait $wait";
+}
+system($command);
+
+my $mergedIntervals = "$outputDir/$outputBam.merged.intervals";
+$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalMerger -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -intervals $indelIntervals -intervals $mismatchIntervals\" -o $mergedIntervals -oarg o -wait $outputDir/$outputBam.intervals -j $outputDir/$outputBam.merged -q $queue";
+if ($dry) {
+    $command .= " -dry";
+}
+system($command);
+
+my $cleanedBam;
+if ($inject) {
+    $cleanedBam = "$outputDir/$outputBam.cleaned.bam";
+} else {
+    $cleanedBam = "$outputDir/$outputBam";
+}
+$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 $inputBam -compress 1";
+if ($inject) {
+    $command .= " -cleanedOnly\" -j $outputDir/$outputBam.cleaned";
+} else {
+    $command .= "\" -j $jobName";
+}
+$command .= "\" -o $cleanedBam -oarg O -wait $outputDir/$outputBam.merged -q $queue -bam -i $mergedIntervals -n 50";
+if ($dry) {
+    $command .= " -dry";
+}
+system($command);
+
+
+if ($inject) {
+    my $bam = "$outputDir/$outputBam";
+    $command = "bsub -q $queue -o $bam.sdout";
+    if ($jobName) {
+	$command .= " -J $jobName";
+    }
+    $command .= " -w \"ended($outputDir/$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 $cleanedBam -compress 1";
+    if ($dry) {
+	print "$command\n";
+    } else {
+	system($command);
+    }
+}
diff --git a/perl/1kgScripts/runPilot1Pipeline.pl b/perl/1kgScripts/runPilot1Pipeline.pl
new file mode 100755
index 000000000..39ece6fb0
--- /dev/null
+++ b/perl/1kgScripts/runPilot1Pipeline.pl
@@ -0,0 +1,64 @@
+#!/usr/bin/perl -w
+
+use strict;
+use Getopt::Long;
+
+sub usage {
+    print "Usage: perl runPilot1Pipeline.pl\n\t-i <input dir>\n\t-o <output directory>\n\t[-sting Sting dir]\n\t[-q farm queue; default:gsa]\n\t[-dry]\n";
+    exit(1);
+}
+
+my $inputDir = undef;
+my $outputDir = undef;
+my $dry;
+my $queue = "gsa";
+my $sting = "/humgen/gsa-scr1/ebanks/Sting";
+
+GetOptions( "i=s" => \$inputDir,
+	    "odir=s" => \$outputDir,
+	    "q:s" => \$queue,
+	    "dry!" => \$dry,
+	    "sting:s" => \$sting );
+
+usage() if ( !$inputDir || !$outputDir );
+
+my @samples = ("ceu","yri","chb_jpt");
+
+foreach my $sample (@samples) {
+
+    $inputBam = "$inputDir/low_coverage_$sample.bam";
+    $outputHead = "$outputDir/$sample";
+    clean($inputBam, $outputDir, "$outputHead.bam", $queue, $sting, $dry);
+#    call($outputBam, $outputHead, $queue, $sting, $dry);
+}
+
+sub clean {
+
+    my $inputBam = $_[0];
+    my $outputDir = $_[1];
+    my $outputBam = $_[2];
+    my $queue = $_[3];
+    my $sting = $_[4];
+    my $dry = $_[5];
+
+    my $cmd = "perl $sting/perl/1kgScripts/runCleaningPipeline.pl -i $inputBam -odir $outputDir -obam $outputBam -q $queue -j $outputBam.cleaningpipeline -sting $sting";
+    if ($dry) {
+	$cmd .= " -dry";
+    }
+    system($cmd);
+}
+
+sub call {
+
+    my $inputBam = $_[0];
+    my $outputHead = $_[1];
+    my $queue = $_[2];
+    my $sting = $_[3];
+    my $dry = $_[4];
+
+    $cmd = "perl $sting/perl/1kgScripts/runCallingPipeline.pl -i $inputBam -o $outputHead -q $queue -wait $inputBam.cleaningpipeline -sting $sting";
+    if ($dry) {
+	$cmd .= " -dry";
+    }
+    system($cmd);
+}
diff --git a/perl/1kgScripts/runPilot2Pipeline.pl b/perl/1kgScripts/runPilot2Pipeline.pl
new file mode 100755
index 000000000..194ac293c
--- /dev/null
+++ b/perl/1kgScripts/runPilot2Pipeline.pl
@@ -0,0 +1,83 @@
+#!/usr/bin/perl -w
+
+use strict;
+use Getopt::Long;
+
+sub usage {
+    print "Usage: perl runPilot2Pipeline.pl\n\t-i <input dir>\n\t-o <output directory>\n\t[-sting Sting dir]\n\t[-q farm queue; default:gsa]\n\t[-dry]\n";
+    exit(1);
+}
+
+my $inputDir = undef;
+my $outputDir = undef;
+my $dry;
+my $queue = "gsa";
+my $sting = "/humgen/gsa-scr1/ebanks/Sting";
+
+GetOptions( "i=s" => \$inputDir,
+	    "odir=s" => \$outputDir,
+	    "q:s" => \$queue,
+	    "dry!" => \$dry,
+	    "sting:s" => \$sting );
+
+usage() if ( !$inputDir || !$outputDir );
+
+my @samples = ("NA19238","NA19239","NA19240","NA12878","NA12891","NA12892");
+
+foreach my $sample (@samples) {
+
+    my $inputBamSLX = "$inputDir/$sample.pilot2.SLX.bam";
+    my $outputHead = "$outputDir/$sample.SLX";
+    clean($inputBamSLX, $outputDir, "$outputHead.bam", $queue, $sting, $dry);
+#    call($outputBam, $outputHead, $queue, $sting, $dry);
+
+    if ($sample eq "NA12878" || $sample eq "NA19240") {
+	my $inputBamSOLID = "$inputDir/$sample.pilot2.SOLID.bam";
+	$outputHead = "$outputDir/$sample.SOLID";
+	clean($inputBamSOLID, $outputDir, "$outputHead.bam", $queue, $sting, $dry);
+#	call($outputBam, $outputHead, $queue, $sting, $dry);
+
+	my $inputBam454 = "$inputDir/$sample.pilot2.454.bam";
+	$outputHead = "$outputDir/$sample.454";
+#	call($inputBam454, $outputHead, $queue, $sting, $dry);
+
+	my @inputBams = ($inputBamSOLID, $inputBam454);
+	$outputHead = "$outputDir/$sample.SOLID_454";
+#	multicall($inputBams, $outputHead, $queue, $sting, $dry);
+
+	@inputBams = ($inputBamSLX, $inputBamSOLID, $inputBam454);
+	$outputHead = "$outputDir/$sample.allTechs";
+#	multicall($inputBams, $outputHead, $queue, $sting, $dry);
+    }
+}
+
+sub clean {
+
+    my $inputBam = $_[0];
+    my $outputDir = $_[1];
+    my $outputBam = $_[2];
+    my $queue = $_[3];
+    my $sting = $_[4];
+    my $dry = $_[5];
+
+    my $cmd = "perl $sting/perl/1kgScripts/runCleaningPipeline.pl -i $inputBam -odir $outputDir -obam $outputBam -q $queue -inject -j $outputBam.cleaningpipeline -sting $sting";
+    if ($dry) {
+	$cmd .= " -dry";
+    }
+    system($cmd);
+}
+
+sub call {
+
+    my $inputBam = $_[0];
+    my $outputHead = $_[1];
+    my $queue = $_[2];
+    my $sting = $_[3];
+    my $dry = $_[4];
+
+    my $cmd = "perl $sting/perl/1kgScripts/runCallingPipeline.pl -i $inputBam -o $outputHead -q $queue -snps -wait $inputBam.cleaningpipeline -sting $sting";
+    if ($dry) {
+	$cmd .= " -dry";
+    }
+    system($cmd);
+}
diff --git a/perl/1kgScripts/runPilotPipelines.sh b/perl/1kgScripts/runPilotPipelines.sh
new file mode 100755
index 000000000..3c3230815
--- /dev/null
+++ b/perl/1kgScripts/runPilotPipelines.sh
@@ -0,0 +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
diff --git a/perl/enqueueGATKjobsByChromosome.pl b/perl/enqueueGATKjobsByChromosome.pl
deleted file mode 100755
index 3685f76ba..000000000
--- a/perl/enqueueGATKjobsByChromosome.pl
+++ /dev/null
@@ -1,111 +0,0 @@
-#!/usr/bin/perl -w
-
-use strict;
-use Getopt::Long;
-
-my $walker = undef;
-my $pilot = "pilot2";
-my $queue = "gsa";
-my $tech = "SLX";
-my $jar = "/humgen/gsa-scr1/ebanks/Sting/dist/GenomeAnalysisTK.jar";
-
-GetOptions( "T=s" => \$walker,
-	    "p:s" => \$pilot,
-	    "q:s" => \$queue,
-	    "tech:s" => \$tech,
-	    "j:s" => \$jar );
-
-exit(1) if ( !$walker );
-
-my @samples;
-if ($pilot eq "pilot1") {
-    @samples = ("CEU","YRI","CHB-JPT");
-} elsif ($pilot eq "pilot2") {
-    @samples = ("NA19238","NA19239","NA19240","NA12878","NA12891","NA12892");
-}
-
-foreach my $sample (@samples) {
-
-    my $num = 1;
-    while ($num < 23) {
-	enqueue($sample, $num, $pilot, $queue, $jar, $walker, $tech);
-	$num++;
-    }
-
-    enqueue($sample, "X", $pilot, $queue, $jar, $walker, $tech);
-    enqueue($sample, "Y", $pilot, $queue, $jar, $walker, $tech);
-}
-
-sub enqueue {
-
-    my $sample = $_[0];
-    my $chr = $_[1];
-    my $pilot = $_[2];
-    my $queue = $_[3];
-    my $jar = $_[4];
-    my $walker = $_[5];
-    my $tech = $_[6];
-
-    my $inputBam;
-    if ($pilot eq "pilot2") {
-	$inputBam = "/broad/1KG/DCC/ftp/pilot_data/$sample/alignment/$sample.chrom$chr.$tech.SRP000032.2009_07.bam";
-    } else {
-	$inputBam = "/broad/hptmp/ebanks/1kg_pilot1/".$sample."_BAMS.list";
-    }
-
-    my $outputDir;
-    if ($pilot eq "pilot1") {
-	$outputDir = "/broad/hptmp/ebanks/1kg_pilot1/cleaned";
-    } else {
-	$outputDir = "/broad/hptmp/ebanks/1kg_pilot2/cleaned";
-    }
-
-    my $cmd;
-    my $outputFile;
-
-  SWITCH: {
-      $walker eq "IndelIntervals" && do {
-	  $outputFile = "$outputDir/intervals/$sample.chr$chr.$tech.indels.intervals";
-	  $cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T IndelIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -o $outputFile -L $chr";
-	  last SWITCH;
-      };
-      $walker eq "MismatchIntervals" && do {
-	  $outputFile = "$outputDir/intervals/$sample.chr$chr.$tech.mismatches.intervals";
-	  $cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T MismatchIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -o $outputFile -L $chr";
-	  last SWITCH;
-      };
-      $walker eq "SNPClusters" && do {
-	  $outputFile = "$outputDir/intervals/$sample.chr$chr.$tech.clusters.intervals";
-	  $cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T SNPClusters -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -o $outputFile -L $chr";
-	  last SWITCH;
-      };
-      $walker eq "IntervalMerger" && do {
-	  $outputFile = "$outputDir/intervals/$sample.chr$chr.$tech.merged.intervals";
-	  $cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T IntervalMerger -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -o $outputFile -L $chr -intervals $outputDir/intervals/$sample.chr$chr.$tech.indels.intervals -intervals $outputDir/intervals/$sample.chr$chr.$tech.mismatches.intervals";
-	  last SWITCH;
-      };
-      $walker eq "IntervalCleaner" && do {
-	  if ($pilot eq "pilot2") {
-	      $outputFile = "$outputDir/cleaner/$sample.chr$chr.$tech.bam";
-	  } else {
-	      $outputFile = "$outputDir/bams/$sample.chr$chr.$tech.bam";
-	  }
-	  $cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -O $outputFile -L $chr -intervals $outputDir/intervals/$sample.chr$chr.$tech.merged.intervals -compress 1";
-	  if ($pilot eq "pilot2") {
-	      $cmd .= " -cleanedOnly";
-	  }
-	  last SWITCH;
-      };
-      $walker eq "CleanedReadInjector" && do {
-	  $outputFile = "$outputDir/bams/$sample.chr$chr.$tech.bam";
-	  $cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T CleanedReadInjector -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -o $outputFile -L $chr";
-	  last SWITCH;
-      };
-
-      print "$walker is not a supported class\n";
-      exit(1);
-    }
-
-#    print "$cmd\n";
-    system($cmd);
-}
diff --git a/perl/splitAndEnqueueGATKjobs.pl b/perl/splitAndEnqueueGATKjobs.pl
new file mode 100755
index 000000000..388c6fed7
--- /dev/null
+++ b/perl/splitAndEnqueueGATKjobs.pl
@@ -0,0 +1,151 @@
+#!/usr/bin/perl -w
+
+# Runs a given GATK walker genome-wide, but splits up the jobs
+# and then merges the results together.  One should really use
+# scatter-gather here, but I wanted to test against that framework
+# (to ensure consistency) so I wrote this temporary script.
+# Also, it allowed me to add in farm commands for wait ids
+# (which is currently unavailable in scatter-gather).
+# If intervals file is left blank, it splits by chromosome.
+
+use strict;
+use Getopt::Long;
+
+sub usage {
+    print "Usage: perl enqueueGATKjobsByChromosome.pl\n\t-cmd <GATK command without output or -L args>\n\t-o <output file>\n\t[-oarg GATK output argument; default:o]\n\t[-i intervals file]\n\t[-n number of splits to make]\n\t[-q farm queue; default:gsa]\n\t[-wait farm wait id]\n\t[-job farm job name]\n\t[-dry]\n\t[-bam is output format bam?; default:no]\n";
+    exit(1);
+}
+
+my $cmd = undef;
+my $output = undef;
+my $outputArg = "o";
+my $jobName = undef;
+my $wait = undef;
+my $queue = "gsa";
+my $breaks = 24;
+my $intervalsFile = undef;
+my $dry;
+my $isBam;
+
+GetOptions( "cmd=s" => \$cmd,
+	    "o=s" => \$output,
+	    "oarg:s" => \$outputArg,
+	    "job:s" => \$jobName,
+	    "wait:s" => \$wait,
+	    "n:i" => \$breaks,
+	    "i:s" => \$intervalsFile,
+	    "dry!" => \$dry,
+	    "bam!" => \$isBam,
+	    "q:s" => \$queue);
+
+usage() if ( !$cmd || !$output );
+
+my @intervals;
+if (!$intervalsFile) {
+    my $num = 1;
+    while ($num < 23) {
+	push(@intervals, $num);
+	$num++;
+    }
+    push(@intervals, "X");
+    push(@intervals, "Y");
+} else {
+    open(FILE, "< $intervalsFile") or die "can't open $intervalsFile: $!";
+    my @lines = <FILE>;
+    chomp(@lines);
+    my $linecount = scalar(@lines);
+    if ($linecount < $breaks) {
+	$breaks = $linecount;
+    }
+
+    my $linesPerJob = $linecount / $breaks;
+    my $index = 0;
+    for (my $i = 1; $i < $breaks; $i++) {
+	my $interval = "";
+	for (my $j = 0; $j < $linesPerJob; $j++) {
+	    $interval .= "$lines[$index];";
+	    $index++;
+	}
+	push(@intervals, $interval);
+    }
+    my $interval = "";
+    while ($index < $linecount) {
+	$interval .= "$lines[$index];";
+	$index++;
+    }
+    push(@intervals, $interval);
+}
+
+my $intervalcount = scalar(@intervals);
+for (my $i = 0; $i < $intervalcount; $i++) {
+    enqueue($intervals[$i], $cmd, $output, $outputArg, $wait, $queue, $dry, $isBam, ($i+1));
+}
+
+mergeResults($output, $queue, $dry, $isBam, $jobName, $intervalcount);
+
+sub enqueue {
+
+    my $interval = $_[0];
+    my $cmd = $_[1];
+    my $outArg = $_[3];
+    my $waitid = $_[4];
+    my $queue = $_[5];
+    my $dry = $_[6];
+    my $bam = $_[7];
+    my $index = $_[8];
+
+    my $output = "$_[2].$index";
+    if ($bam) {
+	$output .= ".bam";
+    }
+
+    my $bsub = "bsub -q $queue -o $output.sdout -J $_[2]";
+    if ($waitid) {
+	$bsub .= " -w \"ended($waitid)\"";
+    }
+
+    my $command = "$bsub $cmd -$outputArg $output -L $interval";
+    execute($command, $dry);
+}
+
+sub mergeResults {
+
+    my $output = $_[0];
+    my $queue = $_[1];
+    my $dry = $_[2];
+    my $bam = $_[3];
+    my $jobName = $_[4];
+    my $intervalcount = $_[5];
+
+    my $cmd = "bsub -q $queue -o $output.sdout -w \"ended($output)\"";
+    if ($jobName) {
+	$cmd .= " -J $jobName";
+    }
+
+    if ($bam) {
+	$cmd .= " samtools merge $output ";
+	for (my $i = 1; $i <= $intervalcount; $i++) {
+	    $cmd .= "$output.$i.bam ";
+	}
+    } else {
+	$cmd .= " cat ";
+	for (my $i = 1; $i <= $intervalcount; $i++) {
+	    $cmd .= "$output.$i ";
+	}
+	$cmd .= "> $output";
+    }
+
+    execute($cmd, $dry);
+}
+
+sub execute {
+
+    my $cmd = $_[0];
+    my $dry = $_[1];
+
+    if ($dry) {
+	print "$cmd\n";
+    } else {
+	system($cmd);
+    }
+}