diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q
index 50474cb7b..060cf588c 100755
--- a/scala/qscript/fullCallingPipeline.q
+++ b/scala/qscript/fullCallingPipeline.q
@@ -206,6 +206,8 @@ class fullCallingPipeline extends QScript {
     snps.jobOutputFile = new File(".queue/logs/SNPCalling/UnifiedGenotyper.out")
     snps.analysisName = base+"_SNP_calls"
     snps.input_file = bamFiles
+    snps.annotation ++= List("AlleleBalance")
+    snps.input_file = bamFiles
     snps.group :+= "Standard"
     snps.out = new File("SnpCalls", base+".vcf")
     snps.standard_min_confidence_threshold_for_emitting = Some(10)
@@ -309,8 +311,8 @@ class fullCallingPipeline extends QScript {
     handFilter.jobOutputFile = new File(".queue/logs/SNPCalling/HandFilter.out")
     handFilter.variantVCF = masker.out
     handFilter.rodBind :+= RodBind("mask", "VCF", mergeIndels.out)
-    handFilter.filterName ++= List("StrandBias","QualByDepth","HomopolymerRun")
-    handFilter.filterExpression ++= List("\"SB>=0.10\"","\"QD<5.0\"","\"HRun>=4\"")
+    handFilter.filterName ++= List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
+    handFilter.filterExpression ++= List("\"SB>=0.10\"","\"AB>=0.75\"","\"QD<5.0\"","\"HRun>=4\"")
     handFilter.out = swapExt("SnpCalls",annotated.out,".vcf",".handfiltered.vcf")
     handFilter.analysisName = base+"_HandFilter"