diff --git a/perl/enqueueGATKcallerJobs.pl b/perl/enqueueGATKcallerJobs.pl
new file mode 100755
index 000000000..fc65c6641
--- /dev/null
+++ b/perl/enqueueGATKcallerJobs.pl
@@ -0,0 +1,67 @@
+#!/usr/bin/perl -w
+
+use strict;
+use Getopt::Long;
+
+my $pilot = "pilot2";
+my $queue = "gsa";
+my $tech = "SLX";
+my $jar = "/humgen/gsa-scr1/ebanks/Sting/dist/GenomeAnalysisTK.jar";
+
+GetOptions( "p:s" => \$pilot,
+	    "q:s" => \$queue,
+	    "tech:s" => \$tech,
+	    "j:s" => \$jar );
+
+my @samples;
+if ($pilot eq "pilot1") {
+    @samples = ("CEU","YRI","CHB-JPT");
+} elsif ($pilot eq "pilot2") {
+    @samples = ("NA19238","NA19239","NA19240","NA12878","NA12891","NA12892");
+}
+
+foreach my $sample (@samples) {
+    enqueue($sample, $pilot, $queue, $jar, $tech);
+}
+
+sub enqueue {
+
+    my $sample = $_[0];
+    my $pilot = $_[1];
+    my $queue = $_[2];
+    my $jar = $_[3];
+    my $tech = $_[4];
+
+    my $inputBamStr = "";
+    my $outputDir;
+    if ($pilot eq "pilot2") {
+	$inputBamStr = "-I /humgen/gsa-hphome1/projects/1kg_pilot2/useTheseBamsForAnalyses/$sample.$tech.bam";
+	$outputDir = "/broad/hptmp/ebanks/1kg_pilot2/cleaned/calls";
+    } else {
+	my $num = 1;
+	while ($num < 23) {
+	    $inputBamStr .= "-I /broad/hptmp/ebanks/1kg_pilot1/cleaned/bams/$sample.chr$num.$tech.bam ";
+	    $num++;
+	}
+	$inputBamStr .= "-I /broad/hptmp/ebanks/1kg_pilot1/cleaned/bams/$sample.chrX.$tech.bam -I /broad/hptmp/ebanks/1kg_pilot1/cleaned/bams/$sample.chrY.$tech.bam ";
+	$outputDir = "/broad/hptmp/ebanks/1kg_pilot1/cleaned/calls";
+    }
+
+    my $outputFile = "$outputDir/indels/$sample.$tech.low.calls";
+    my $cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -o $outputFile -minConsensusFraction 0.5 -minFraction 0.";
+    if ($pilot eq "pilot1") { $cmd .= "0"; }
+    $cmd .= "1 -minCnt 2 -1kg";
+    system($cmd);
+
+    $outputFile = "$outputDir/indels/$sample.$tech.high.calls";
+    $cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T IndelGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -o $outputFile -minConsensusFraction 0.5 -minFraction 0.";
+    if ($pilot eq "pilot1") { $cmd .= "0"; }
+    $cmd .= "3 -minCnt 2 -1kg";
+    system($cmd);
+
+    if ($pilot eq "pilot2") {
+	$outputFile = "$outputDir/unfiltered_snps/$sample.$tech.geli.calls";
+	$cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T SingleSampleGenotyper -R /broad/1KG/reference/human_b36_both.fasta $inputBamStr -varout $outputFile -lod 5";
+	system($cmd);
+    }
+}
diff --git a/perl/enqueueGATKjobsByChromosome.pl b/perl/enqueueGATKjobsByChromosome.pl
new file mode 100755
index 000000000..3685f76ba
--- /dev/null
+++ b/perl/enqueueGATKjobsByChromosome.pl
@@ -0,0 +1,111 @@
+#!/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);
+}