diff --git a/lua/MergeIntervals.lua b/lua/MergeIntervals.lua
index 88c06a990..0a505c302 100644
--- a/lua/MergeIntervals.lua
+++ b/lua/MergeIntervals.lua
@@ -9,9 +9,17 @@
 
 assert(table.getn(arg) > 0, "\n\nMissing input file\n\nUsage:\n\tlua MergeIntervals.lua raw.intervals > merged.intervals\n\n")
 
+
+local function comp(a, b)
+   if tonumber(a) and tonumber(b) then return tonumber(a) < tonumber(b) end
+   return a<b
+end
+
+
 -- read file and create chromosome tables with raw intervals marked as "x"
 local intervals = {}
 local intervalKeys = {}
+local sortedChrs = {}
 for l in io.lines(arg[1]) do
 	local chr, a, b = l:match("([%a%d]+):(%d+)-(%d+)")
 	a,b = tonumber(a), tonumber(b)
@@ -20,6 +28,7 @@ for l in io.lines(arg[1]) do
 		intervals[chr].min = a
 		intervals[chr].max = b
 		intervalKeys[chr] = {}
+		table.insert(sortedChrs, chr)
 	end
 	for i=a,b do intervals[chr][i] = "x" end
 	intervals[chr].min = math.min(intervals[chr].min, a)
@@ -51,9 +60,10 @@ for c, chrTable in pairs(intervals) do
 	end
 end
 
-for c,v in pairs(intervalsIndex) do
-	table.sort(v)
-	for _,intervalStart in ipairs(v) do
+table.sort(sortedChrs, comp)
+for _,c in pairs(sortedChrs) do
+	table.sort(intervalsIndex[c])
+	for _,intervalStart in ipairs(intervalsIndex[c]) do
 		if intervalSize[c][intervalStart] > 0 then 
 			print(c..":"..intervalStart.."-"..intervalStart + intervalSize[c][intervalStart])
 		end
diff --git a/scala/qscript/oneoffs/carneiro/pbCalling.scala b/scala/qscript/oneoffs/carneiro/pbCalling.scala
index ee1d29a55..6141855ed 100755
--- a/scala/qscript/oneoffs/carneiro/pbCalling.scala
+++ b/scala/qscript/oneoffs/carneiro/pbCalling.scala
@@ -1,3 +1,4 @@
+import org.broadinstitute.sting.gatk.CommandLineGATK
 import org.broadinstitute.sting.queue.extensions.gatk._
 import org.broadinstitute.sting.queue.QScript
 
@@ -110,16 +111,24 @@ class pbCalling extends QScript {
               "/seq/references/HybSelOligos/whole_exome_agilent_1.1_refseq_plus_3_boosters/whole_exome_agilent_1.1_refseq_plus_3_boosters.Homo_sapiens_assembly19.targets.interval_list", 2.6, !lowPass),
     "pacbio" -> new Target("pacbio", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37,
               new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/pacbio.recal.bam"),
-              new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/amplicon/pacbio.filtered.vcf"),
+              new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/pacbio.filtered.vcf"),
 				      "/humgen/gsa-scr1/carneiro/prj/pacbio/data/pacbio.hg19.intervals", 1.8, !lowPass),
     "pb200" -> new Target("pb200", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37,
               new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb200.recal.bam"),
-              new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/amplicon/pb200.filtered.vcf"),
+              new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/pb200.filtered.vcf"),
 				      "/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb200.hg19.intervals", 1.8, !lowPass),
     "pb2k" -> new Target("pb2k", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37,
               new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb2k.recal.bam"),
-              new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/amplicon/pb2k.filtered.vcf"),
-				      "/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb2k.hg19.intervals", 1.8, !lowPass)
+              new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/pb2k.filtered.vcf"),
+				      "/humgen/gsa-scr1/carneiro/prj/pacbio/data/pb2k.hg19.intervals", 1.8, !lowPass),
+    "cc200" -> new Target("cc200", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37,
+              new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc200.recal.bam"),
+              new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/cc200.filtered.vcf"),
+				      "/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc200.hg19.intervals", 1.8, !lowPass),
+    "cc2k" -> new Target("cc2k", b37, dbSNP_b37_129, hapmap_b37, indelMask_b37,
+              new File("/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc2k.recal.bam"),
+              new File("/humgen/gsa-scr1/carneiro/prj/pacbio/analisys/snps/cc2k.filtered.vcf"),
+				      "/humgen/gsa-scr1/carneiro/prj/pacbio/data/cc2k.hg19.intervals", 1.8, !lowPass)
   )
 
 
@@ -245,7 +254,7 @@ class pbCalling extends QScript {
       this.tranchesFile = t.tsTranchesFile
   }
 
-  // 5.) Variant Cut (OPTIONAL!) filter out the variants marked by recalibration to the 99% tranche
+  // 5.) Variant Cut filter out the variants marked by recalibration to the 99% tranche
   class VariantCut(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.ApplyVariantCuts with UNIVERSAL_GATK_ARGS {
       this.reference_sequence = t.reference
       this.rodBind :+= RodBind("input", "VCF",  t.tsRecalibratedVCF )
@@ -260,8 +269,8 @@ class pbCalling extends QScript {
         this.rodBind :+= RodBind("dbsnp", "VCF", t.dbsnpFile)
   }
 
-  // 6.) Variant Evaluation (OPTIONAL!) based on the sensitivity recalibrated vcf
-  class VariantEvaluation(t: Target) extends VariantEval with UNIVERSAL_GATK_ARGS {
+  // 6.) Variant Evaluation  based on the sensitivity recalibrated vcf
+  class VariantEvaluation(t: Target) extends org.broadinstitute.sting.queue.extensions.gatk.VariantEval with UNIVERSAL_GATK_ARGS {
       val name: String = t.name
       this.reference_sequence = t.reference
       this.rodBind :+= RodBind("comphapmap", "VCF", t.hapmapFile)