diff --git a/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java b/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java
index 0244434b4..45b190537 100644
--- a/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java
+++ b/java/src/net/sf/picard/reference/FastaSequenceIndexBuilder.java
@@ -26,7 +26,7 @@
 package net.sf.picard.reference;
 
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceDataSourceProgressListener;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import static net.sf.picard.reference.FastaSequenceIndexBuilder.Status.*;
 
@@ -215,7 +215,7 @@ public class FastaSequenceIndexBuilder {
             throw new UserException.CouldNotReadInputFile(fastaFile, String.format("Could not read fasta file"), e);
         }
         catch (Exception e) {
-            throw new GATKException(e.getMessage(), e);
+            throw new ReviewedStingException(e.getMessage(), e);
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/alignment/Alignment.java b/java/src/org/broadinstitute/sting/alignment/Alignment.java
index 98a8ed9c1..a70be0006 100644
--- a/java/src/org/broadinstitute/sting/alignment/Alignment.java
+++ b/java/src/org/broadinstitute/sting/alignment/Alignment.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.alignment;
 
 import net.sf.samtools.*;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.utils.Utils;
 
@@ -189,7 +189,7 @@ public class Alignment {
             read = (SAMRecord)unmappedRead.clone();
         }
         catch(CloneNotSupportedException ex) {
-            throw new GATKException("Unable to create aligned read from template.");
+            throw new ReviewedStingException("Unable to create aligned read from template.");
         }
 
         if(newSAMHeader != null)
diff --git a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
index f6a40ec9d..16e713bf6 100644
--- a/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/alignment/AlignmentValidationWalker.java
@@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
@@ -120,7 +120,7 @@ public class AlignmentValidationWalker extends ReadWalker<Integer,Integer> {
                     logger.error(String.format("    Mapping quality: %s%n", alignmentsByScore[i].getMappingQuality()));
                 }
             }
-            throw new GATKException(String.format("Read %s mismatches!", read.getReadName()));
+            throw new ReviewedStingException(String.format("Read %s mismatches!", read.getReadName()));
         }
 
         return 1;
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java b/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
index 0dacfb460..cd7800900 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/BWTFiles.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.alignment.bwa;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 import org.broadinstitute.sting.alignment.reference.bwt.BWT;
@@ -75,7 +75,7 @@ public class BWTFiles {
      */
     public BWTFiles(String prefix) {
         if(prefix == null)
-            throw new GATKException("Prefix must not be null.");
+            throw new ReviewedStingException("Prefix must not be null.");
         annFile = new File(prefix + ".ann");
         ambFile = new File(prefix + ".amb");
         pacFile = new File(prefix + ".pac");
@@ -134,7 +134,7 @@ public class BWTFiles {
             success &= reverseSAFile.delete();
 
             if(!success)
-                throw new GATKException("Unable to clean up autogenerated representation");
+                throw new ReviewedStingException("Unable to clean up autogenerated representation");
         }
     }
 
@@ -182,7 +182,7 @@ public class BWTFiles {
             writeEncodedReferenceSequence(reverseReferenceSequence,rpacFile,rbwtFile,rsaFile);
         }
         catch(IOException ex) {
-            throw new GATKException("Unable to write autogenerated reference sequence to temporary files");
+            throw new ReviewedStingException("Unable to write autogenerated reference sequence to temporary files");
         }
 
         // Make sure that, at the very least, all temporary files are deleted on exit.
@@ -228,13 +228,13 @@ public class BWTFiles {
      * Convert the given reference sequence into a form suitable for building into
      * on-the-fly sequences.
      * @param referenceSequence The reference sequence to normalize.
-     * @throws GATKException if normalized sequence cannot be generated.
+     * @throws org.broadinstitute.sting.utils.exceptions.ReviewedStingException if normalized sequence cannot be generated.
      */
     private static void normalizeReferenceSequence(byte[] referenceSequence) {
         StringUtil.toUpperCase(referenceSequence);
         for(byte base: referenceSequence) {
             if(base != 'A' && base != 'C' && base != 'G' && base != 'T')
-                throw new GATKException(String.format("Base type %c is not supported when building references on-the-fly",(char)base));
+                throw new ReviewedStingException(String.format("Base type %c is not supported when building references on-the-fly",(char)base));
         }
     }
 }
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
index 8c9fba53e..322dd01b6 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/c/BWACAligner.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.alignment.bwa.c;
 
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileHeader;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.alignment.bwa.BWAConfiguration;
 import org.broadinstitute.sting.alignment.bwa.BWTFiles;
@@ -29,15 +29,15 @@ public class BWACAligner extends BWAAligner {
     public BWACAligner(BWTFiles bwtFiles, BWAConfiguration configuration) {
         super(bwtFiles,configuration);
         if(thunkPointer != 0)
-            throw new GATKException("BWA/C attempting to reinitialize.");
+            throw new ReviewedStingException("BWA/C attempting to reinitialize.");
 
-        if(!bwtFiles.annFile.exists()) throw new GATKException("ANN file is missing; please rerun 'bwa aln' to regenerate it.");
-        if(!bwtFiles.ambFile.exists()) throw new GATKException("AMB file is missing; please rerun 'bwa aln' to regenerate it.");
-        if(!bwtFiles.pacFile.exists()) throw new GATKException("PAC file is missing; please rerun 'bwa aln' to regenerate it.");
-        if(!bwtFiles.forwardBWTFile.exists()) throw new GATKException("Forward BWT file is missing; please rerun 'bwa aln' to regenerate it.");
-        if(!bwtFiles.forwardSAFile.exists()) throw new GATKException("Forward SA file is missing; please rerun 'bwa aln' to regenerate it.");
-        if(!bwtFiles.reverseBWTFile.exists()) throw new GATKException("Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it.");
-        if(!bwtFiles.reverseSAFile.exists()) throw new GATKException("Reverse SA file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.annFile.exists()) throw new ReviewedStingException("ANN file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.ambFile.exists()) throw new ReviewedStingException("AMB file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.pacFile.exists()) throw new ReviewedStingException("PAC file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.forwardBWTFile.exists()) throw new ReviewedStingException("Forward BWT file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.forwardSAFile.exists()) throw new ReviewedStingException("Forward SA file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.reverseBWTFile.exists()) throw new ReviewedStingException("Reverse BWT file is missing; please rerun 'bwa aln' to regenerate it.");
+        if(!bwtFiles.reverseSAFile.exists()) throw new ReviewedStingException("Reverse SA file is missing; please rerun 'bwa aln' to regenerate it.");
 
         thunkPointer = create(bwtFiles,configuration);
     }
@@ -60,7 +60,7 @@ public class BWACAligner extends BWAAligner {
     @Override
     public void updateConfiguration(BWAConfiguration configuration) {
         if(thunkPointer != 0)
-            throw new GATKException("BWA/C: attempting to update configuration of uninitialized aligner.");
+            throw new ReviewedStingException("BWA/C: attempting to update configuration of uninitialized aligner.");
         updateConfiguration(thunkPointer,configuration);
     }
 
@@ -70,7 +70,7 @@ public class BWACAligner extends BWAAligner {
     @Override
     public void close() {
         if(thunkPointer == 0)
-            throw new GATKException("BWA/C close attempted, but BWA/C is not properly initialized.");
+            throw new ReviewedStingException("BWA/C close attempted, but BWA/C is not properly initialized.");
         destroy(thunkPointer);
     }
 
@@ -82,7 +82,7 @@ public class BWACAligner extends BWAAligner {
     @Override
     public Alignment getBestAlignment(final byte[] bases) {
         if(thunkPointer == 0)
-            throw new GATKException("BWA/C getBestAlignment attempted, but BWA/C is not properly initialized.");
+            throw new ReviewedStingException("BWA/C getBestAlignment attempted, but BWA/C is not properly initialized.");
         return getBestAlignment(thunkPointer,bases);
     }
 
@@ -193,7 +193,7 @@ public class BWACAligner extends BWAAligner {
      */
     public BWAPath[] getPaths(byte[] bases) {
         if(thunkPointer == 0)
-            throw new GATKException("BWA/C getPaths attempted, but BWA/C is not properly initialized.");
+            throw new ReviewedStingException("BWA/C getPaths attempted, but BWA/C is not properly initialized.");
         return getPaths(thunkPointer,bases);
     }
 
@@ -226,7 +226,7 @@ public class BWACAligner extends BWAAligner {
      */
     protected Alignment[] convertPathsToAlignments(byte[] bases, BWAPath[] paths) {
         if(thunkPointer == 0)
-            throw new GATKException("BWA/C convertPathsToAlignments attempted, but BWA/C is not properly initialized.");
+            throw new ReviewedStingException("BWA/C convertPathsToAlignments attempted, but BWA/C is not properly initialized.");
         return convertPathsToAlignments(thunkPointer,bases,paths);
     }
 
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
index 633d281a6..ae6e22221 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignerTestHarness.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.alignment.bwa.java;
 
 import org.broadinstitute.sting.alignment.Aligner;
 import org.broadinstitute.sting.alignment.Alignment;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.BaseUtils;
 
 import java.io.File;
@@ -61,7 +61,7 @@ public class AlignerTestHarness {
                 alignmentCleaned = (SAMRecord)read.clone();
             }
             catch( CloneNotSupportedException ex ) {
-                throw new GATKException("SAMRecord clone not supported", ex);
+                throw new ReviewedStingException("SAMRecord clone not supported", ex);
             }
 
             if( alignmentCleaned.getReadNegativeStrandFlag() )
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
index 503b406a6..879ecb5fb 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/AlignmentMatchSequence.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.Deque;
 import java.util.ArrayDeque;
@@ -32,7 +32,7 @@ public class AlignmentMatchSequence implements Cloneable {
             copy = (AlignmentMatchSequence)super.clone(); 
         }
         catch( CloneNotSupportedException ex ) {
-            throw new GATKException("Unable to clone AlignmentMatchSequence.");
+            throw new ReviewedStingException("Unable to clone AlignmentMatchSequence.");
         }
 
         copy.entries = new ArrayDeque<AlignmentMatchSequenceEntry>();
@@ -52,7 +52,7 @@ public class AlignmentMatchSequence implements Cloneable {
                 case MATCH_MISMATCH: operator = CigarOperator.MATCH_OR_MISMATCH; break;
                 case INSERTION: operator = CigarOperator.INSERTION; break;
                 case DELETION: operator = CigarOperator.DELETION; break;
-                default: throw new GATKException("convertToCigar: cannot process state: " + entry.getAlignmentState());
+                default: throw new ReviewedStingException("convertToCigar: cannot process state: " + entry.getAlignmentState());
             }
             cigar.add( new CigarElement(entry.count,operator) );
         }
@@ -128,7 +128,7 @@ public class AlignmentMatchSequence implements Cloneable {
                 return (AlignmentMatchSequenceEntry)super.clone(); 
             }
             catch( CloneNotSupportedException ex ) {
-                throw new GATKException("Unable to clone AlignmentMatchSequenceEntry.");
+                throw new ReviewedStingException("Unable to clone AlignmentMatchSequenceEntry.");
             }
         }
 
diff --git a/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java b/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
index e86ea858e..c59546bbb 100644
--- a/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
+++ b/java/src/org/broadinstitute/sting/alignment/bwa/java/BWAAlignment.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.alignment.bwa.java;
 
 import org.broadinstitute.sting.alignment.Alignment;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import net.sf.samtools.Cigar;
 
 /**
@@ -148,7 +148,7 @@ public class BWAAlignment extends Alignment implements Cloneable {
             newAlignment = (BWAAlignment)super.clone();
         }
         catch( CloneNotSupportedException ex ) {
-            throw new GATKException("Unable to clone BWAAlignment.");
+            throw new ReviewedStingException("Unable to clone BWAAlignment.");
         }
         newAlignment.creationNumber = numCreated++;
         newAlignment.alignmentMatchSequence = alignmentMatchSequence.clone();
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java
index 96ec794ce..7f8c48253 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWT.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 /**
  * Represents the Burrows-Wheeler Transform of a reference sequence.
@@ -124,7 +124,7 @@ public class BWT {
      */
     protected byte getBase(long index) {
         if(index == inverseSA0)
-            throw new GATKException(String.format("Base at index %d does not have a text representation",index));
+            throw new ReviewedStingException(String.format("Base at index %d does not have a text representation",index));
 
         SequenceBlock block = getSequenceBlock(index);
         int position = getSequencePosition(index);
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
index b4e095433..64a595419 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTReader.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.BasePackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
@@ -28,7 +28,7 @@ public class BWTReader {
             this.inputStream = new FileInputStream(inputFile);
         }
         catch( FileNotFoundException ex ) {
-            throw new GATKException("Unable to open input file", ex);
+            throw new ReviewedStingException("Unable to open input file", ex);
         }
     }
 
@@ -66,7 +66,7 @@ public class BWTReader {
             }
         }
         catch( IOException ex ) {
-            throw new GATKException("Unable to read BWT from input stream.", ex);
+            throw new ReviewedStingException("Unable to read BWT from input stream.", ex);
         }
 
         return new BWT(inverseSA0, new Counts(count,true), sequenceBlocks);
@@ -80,7 +80,7 @@ public class BWTReader {
             inputStream.close();
         }
         catch( IOException ex ) {
-            throw new GATKException("Unable to close input file", ex);
+            throw new ReviewedStingException("Unable to close input file", ex);
         }
     }
 }
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
index f8f7782ac..b3867ebfe 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/BWTWriter.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
 import org.broadinstitute.sting.alignment.reference.packing.BasePackedOutputStream;
 
@@ -28,7 +28,7 @@ public class BWTWriter {
             this.outputStream = new BufferedOutputStream(new FileOutputStream(outputFile));
         }
         catch( FileNotFoundException ex ) {
-            throw new GATKException("Unable to open output file", ex);
+            throw new ReviewedStingException("Unable to open output file", ex);
         }
     }
 
@@ -53,7 +53,7 @@ public class BWTWriter {
             intPackedOutputStream.write(bwt.counts.toArray(false));
         }
         catch( IOException ex ) {
-            throw new GATKException("Unable to read BWT from input stream.", ex);
+            throw new ReviewedStingException("Unable to read BWT from input stream.", ex);
         }
     }
 
@@ -65,7 +65,7 @@ public class BWTWriter {
             outputStream.close();
         }
         catch( IOException ex ) {
-            throw new GATKException("Unable to close input file", ex);
+            throw new ReviewedStingException("Unable to close input file", ex);
         }
     }
 }
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
index 1a1e5e3ca..bc0a5b63d 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Bases.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.*;
 
@@ -87,7 +87,7 @@ public class Bases implements Iterable<Byte>
             if( entry.getValue().equals(ascii) )
                 return entry.getKey();
         }
-        throw new GATKException(String.format("Base %c is an invalid base to pack", (char)ascii));
+        throw new ReviewedStingException(String.format("Base %c is an invalid base to pack", (char)ascii));
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java
index fc06f4136..268b11ac4 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/Counts.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.HashMap;
 import java.util.Map;
@@ -96,7 +96,7 @@ public class Counts implements Cloneable {
             other = (Counts)super.clone();
         }
         catch(CloneNotSupportedException ex) {
-            throw new GATKException("Unable to clone counts object", ex);
+            throw new ReviewedStingException("Unable to clone counts object", ex);
         }
         other.counts = new HashMap<Byte,Long>(counts);
         other.cumulativeCounts = new HashMap<Byte,Long>(cumulativeCounts);
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
index a78e8633b..92bb713f0 100755
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/CreateBWTFromReference.java
@@ -31,7 +31,7 @@ import net.sf.picard.reference.ReferenceSequence;
 
 import java.io.*;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 
 /**
@@ -182,7 +182,7 @@ public class CreateBWTFromReference {
 
         for( int i = 0; i < bwt.length(); i++ ) {
             if( bwtSequence[i] != existingBWTSequence[i] )
-                throw new GATKException("BWT mismatch at " + i);
+                throw new ReviewedStingException("BWT mismatch at " + i);
         }
 
         File existingSAFile = new File(inputFileName+".sa");
@@ -193,7 +193,7 @@ public class CreateBWTFromReference {
             if( i % 10000 == 0 )
                 System.out.printf("Validating suffix array entry %d%n", i);
             if( suffixArray.get(i) != existingSuffixArray.get(i) )
-                throw new GATKException(String.format("Suffix array mismatch at %d; SA is %d; should be %d",i,existingSuffixArray.get(i),suffixArray.get(i)));
+                throw new ReviewedStingException(String.format("Suffix array mismatch at %d; SA is %d; should be %d",i,existingSuffixArray.get(i),suffixArray.get(i)));
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
index 48868895d..dba3633d1 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArray.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.Comparator;
 import java.util.TreeSet;
@@ -53,7 +53,7 @@ public class SuffixArray {
         this.bwt = bwt;
 
         if(sequenceInterval != 1 && bwt == null)
-            throw new GATKException("A BWT must be provided if the sequence interval is not 1");
+            throw new ReviewedStingException("A BWT must be provided if the sequence interval is not 1");
     }
 
     /**
@@ -118,7 +118,7 @@ public class SuffixArray {
                 inverseSA0 = i;
         }
         if(inverseSA0 < 0)
-            throw new GATKException("Unable to find first inverse SA entry in generated suffix array.");
+            throw new ReviewedStingException("Unable to find first inverse SA entry in generated suffix array.");
 
         return new SuffixArray(inverseSA0,occurrences,suffixArray);
     }    
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
index 4fb983a5b..c10984145 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayReader.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedInputStream;
 import org.broadinstitute.sting.alignment.reference.packing.PackUtils;
 
@@ -35,7 +35,7 @@ public class SuffixArrayReader {
             this.bwt = bwt;
         }
         catch( FileNotFoundException ex ) {
-            throw new GATKException("Unable to open input file", ex);
+            throw new ReviewedStingException("Unable to open input file", ex);
         }
     }
 
@@ -61,7 +61,7 @@ public class SuffixArrayReader {
             uintPackedInputStream.read(suffixArray);
         }
         catch( IOException ex ) {
-            throw new GATKException("Unable to read BWT from input stream.", ex);
+            throw new ReviewedStingException("Unable to read BWT from input stream.", ex);
         }
 
         return new SuffixArray(inverseSA0, new Counts(occurrences,true), suffixArray, suffixArrayInterval, bwt);
@@ -76,7 +76,7 @@ public class SuffixArrayReader {
             inputStream.close();
         }
         catch( IOException ex ) {
-            throw new GATKException("Unable to close input file", ex);
+            throw new ReviewedStingException("Unable to close input file", ex);
         }
     }    
 }
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
index febb87f8f..972fc2a15 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/bwt/SuffixArrayWriter.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.bwt;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.alignment.reference.packing.UnsignedIntPackedOutputStream;
 
 import java.io.*;
@@ -27,7 +27,7 @@ public class SuffixArrayWriter {
             this.outputStream = new BufferedOutputStream(new FileOutputStream(outputFile));
         }
         catch( FileNotFoundException ex ) {
-            throw new GATKException("Unable to open input file", ex);
+            throw new ReviewedStingException("Unable to open input file", ex);
         }
     }
 
@@ -48,7 +48,7 @@ public class SuffixArrayWriter {
             uintPackedOutputStream.write(suffixArray.sequence,1,suffixArray.sequence.length-1);
         }
         catch( IOException ex ) {
-            throw new GATKException("Unable to read BWT from input stream.", ex);
+            throw new ReviewedStingException("Unable to read BWT from input stream.", ex);
         }
     }
 
@@ -61,7 +61,7 @@ public class SuffixArrayWriter {
             outputStream.close();
         }
         catch( IOException ex ) {
-            throw new GATKException("Unable to close input file", ex);
+            throw new ReviewedStingException("Unable to close input file", ex);
         }
     }
 }
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
index c3291774e..6681e37ec 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedInputStream.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
 import java.nio.ByteOrder;
@@ -51,7 +51,7 @@ public class BasePackedInputStream<T> {
 
     public BasePackedInputStream( Class<T> type, FileInputStream inputStream, ByteOrder byteOrder ) {
         if( type != Integer.class )
-            throw new GATKException("Only bases packed into 32-bit words are currently supported by this input stream.  Type specified: " + type.getName());
+            throw new ReviewedStingException("Only bases packed into 32-bit words are currently supported by this input stream.  Type specified: " + type.getName());
         this.type = type;
         this.targetInputStream = inputStream;
         this.targetInputChannel = inputStream.getChannel();
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java
index cfdb10949..c62f40e51 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/BasePackedOutputStream.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
 import java.nio.ByteBuffer;
@@ -134,7 +134,7 @@ public class BasePackedOutputStream<T> {
         else if( type == Byte.class )
             buffer.put((byte)packedBases);
         else
-            throw new GATKException("Cannot pack bases into type " + type.getName());
+            throw new ReviewedStingException("Cannot pack bases into type " + type.getName());
         targetOutputStream.write(buffer.array());        
     }
 }
diff --git a/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java b/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
index 3ab0b7589..beed21b49 100644
--- a/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
+++ b/java/src/org/broadinstitute/sting/alignment/reference/packing/PackUtils.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.alignment.reference.packing;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.IOException;
@@ -58,14 +58,14 @@ public class PackUtils {
             long typeSize = type.getField("MAX_VALUE").getLong(null) - type.getField("MIN_VALUE").getLong(null)+1;
             long intTypeSize = (long)Integer.MAX_VALUE - (long)Integer.MIN_VALUE + 1;
             if( typeSize > intTypeSize )
-                throw new GATKException("Cannot determine number of bits available in type: " + type.getName());
+                throw new ReviewedStingException("Cannot determine number of bits available in type: " + type.getName());
             return (int)(Math.log(typeSize)/Math.log(2));
         }
         catch( NoSuchFieldException ex ) {
-            throw new GATKException("Cannot determine number of bits available in type: " + type.getName(),ex);
+            throw new ReviewedStingException("Cannot determine number of bits available in type: " + type.getName(),ex);
         }
         catch( IllegalAccessException ex ) {
-            throw new GATKException("Cannot determine number of bits available in type: " + type.getName(),ex);
+            throw new ReviewedStingException("Cannot determine number of bits available in type: " + type.getName(),ex);
         }
     }
 
@@ -85,7 +85,7 @@ public class PackUtils {
             case 'T':
                 return 3;
             default:
-                throw new GATKException("Unknown base type: " + base);
+                throw new ReviewedStingException("Unknown base type: " + base);
         }
     }
 
@@ -105,7 +105,7 @@ public class PackUtils {
             case 3:
                 return 'T';
             default:
-                throw new GATKException("Unknown pack type: " + pack);
+                throw new ReviewedStingException("Unknown pack type: " + pack);
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
index 6ae6bc053..c36a8e04f 100644
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitionGroup.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.List;
 import java.util.Collections;
@@ -69,7 +69,7 @@ public class ArgumentDefinitionGroup implements Iterable<ArgumentDefinition> {
      */
     public ArgumentDefinitionGroup merge( ArgumentDefinitionGroup other ) {
         if( !groupNameMatches(other) )
-            throw new GATKException("Unable to merge two argument groups with differing names.");
+            throw new ReviewedStingException("Unable to merge two argument groups with differing names.");
 
         // Create a merged definition group.
         List<ArgumentDefinition> mergedDefinitions = new ArrayList<ArgumentDefinition>();
diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
index 88503eacd..39e698ca3 100755
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentDefinitions.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.Set;
 import java.util.HashSet;
@@ -56,9 +56,9 @@ public class ArgumentDefinitions implements Iterable<ArgumentDefinition> {
             if( definition.fullName.length() == 0 )
                 throw new IllegalArgumentException( "Argument cannot have 0-length fullname." );
             if( hasArgumentDefinition( definition.fullName, FullNameDefinitionMatcher ) )
-                throw new GATKException("Duplicate definition of argument with full name: " + definition.fullName);
+                throw new ReviewedStingException("Duplicate definition of argument with full name: " + definition.fullName);
             if( definition.shortName != null && hasArgumentDefinition( definition.shortName, ShortNameDefinitionMatcher ) )
-                throw new GATKException("Duplicate definition of argument with short name: " + definition.shortName);
+                throw new ReviewedStingException("Duplicate definition of argument with short name: " + definition.shortName);
 
             argumentDefinitions.add( definition );
         }
diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java b/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java
index 9b21def56..fe33ab382 100644
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentIOType.java
@@ -24,7 +24,7 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.lang.annotation.Annotation;
 
@@ -46,6 +46,6 @@ public enum ArgumentIOType {
         for (ArgumentIOType ioType: ArgumentIOType.values())
             if (ioType.annotationClass.isAssignableFrom(annotation.getClass()))
                 return ioType;
-        throw new GATKException("Unknown annotation type: " + annotation);
+        throw new ReviewedStingException("Unknown annotation type: " + annotation);
     }
 }
diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java b/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
index fedbe815c..937c9549a 100644
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentSource.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.lang.reflect.Field;
 import java.util.Arrays;
@@ -208,7 +208,7 @@ public class ArgumentSource {
      */
     public MultiplexArgumentTypeDescriptor createDependentTypeDescriptor(Object containingObject) {
         if(!isDependent())
-            throw new GATKException("Field " + field.getName() + " is independent; no dependent type descriptor can be derived.");
+            throw new ReviewedStingException("Field " + field.getName() + " is independent; no dependent type descriptor can be derived.");
         return ((MultiplexArgumentTypeDescriptor)typeDescriptor).createCustomTypeDescriptor(this,containingObject);
     }
 
diff --git a/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java b/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
index 8eea131e1..a7090f299 100644
--- a/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
+++ b/java/src/org/broadinstitute/sting/commandline/ArgumentTypeDescriptor.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.gatk.walkers.Multiplex;
 import org.broadinstitute.sting.gatk.walkers.Multiplexer;
@@ -83,7 +83,7 @@ public abstract class ArgumentTypeDescriptor {
             if( descriptor.supports(type) )
                 return descriptor;
         }
-        throw new GATKException("Can't process command-line arguments of type: " + type.getName());
+        throw new ReviewedStingException("Can't process command-line arguments of type: " + type.getName());
     }
 
     /**
@@ -265,7 +265,7 @@ public abstract class ArgumentTypeDescriptor {
         for (Class annotation: ARGUMENT_ANNOTATIONS)
             if (source.field.isAnnotationPresent(annotation))
                 return source.field.getAnnotation(annotation);
-        throw new GATKException("ArgumentAnnotation is not present for the argument field: " + source.field.getName());
+        throw new ReviewedStingException("ArgumentAnnotation is not present for the argument field: " + source.field.getName());
     }
 
     /**
@@ -333,7 +333,7 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                 for (Object val : vals) {
                     if (String.valueOf(val).equalsIgnoreCase(value)) return val;
                     try { if (type.getField(val.toString()).isAnnotationPresent(EnumerationArgumentDefault.class)) defaultEnumeration = val; }
-                    catch (NoSuchFieldException e) { throw new GATKException("parsing " + type.toString() + "doesn't contain the field " + val.toString()); }
+                    catch (NoSuchFieldException e) { throw new ReviewedStingException("parsing " + type.toString() + "doesn't contain the field " + val.toString()); }
                 }
                 // if their argument has no value (null), and there's a default, return that default for the enum value
                 if (defaultEnumeration != null && value == null)
@@ -349,7 +349,7 @@ class SimpleArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                 result = ctor.newInstance(value);
             }
         } catch (InvocationTargetException e) {
-            throw new GATKException("constructFromString:InvocationTargetException: Failed conversion - this is most likely caused by using an incorrect data type (e.g. a double when an int is required)");
+            throw new ReviewedStingException("constructFromString:InvocationTargetException: Failed conversion - this is most likely caused by using an incorrect data type (e.g. a double when an int is required)");
         } catch (Exception e) {
             throw new DynamicClassResolutionException(String.class, e);
         }
@@ -416,11 +416,11 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             }
             catch (InstantiationException e) {
                 logger.fatal("ArgumentParser: InstantiationException: cannot convert field " + source.field.getName());
-                throw new GATKException("constructFromString:InstantiationException: Failed conversion " + e.getMessage());
+                throw new ReviewedStingException("constructFromString:InstantiationException: Failed conversion " + e.getMessage());
             }
             catch (IllegalAccessException e) {
                 logger.fatal("ArgumentParser: IllegalAccessException: cannot convert field " + source.field.getName());
-                throw new GATKException("constructFromString:IllegalAccessException: Failed conversion " + e.getMessage());
+                throw new ReviewedStingException("constructFromString:IllegalAccessException: Failed conversion " + e.getMessage());
             }
 
             for( ArgumentMatch match: matches ) {
@@ -452,7 +452,7 @@ class CompoundArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             }
         }
         else
-            throw new GATKException("Unsupported compound argument type: " + type);
+            throw new ReviewedStingException("Unsupported compound argument type: " + type);
 
         // WARNING: Side effect!
         parsingEngine.addTags(result,tags);
@@ -520,7 +520,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     @Override
     public Object createTypeDefault(ArgumentSource source,Class type) {
         if(multiplexer == null || multiplexedIds == null)
-            throw new GATKException("No multiplexed ids available");
+            throw new ReviewedStingException("No multiplexed ids available");
 
         Map<Object,Object> multiplexedMapping = new HashMap<Object,Object>();
         Class componentType = getCollectionComponentType(source.field);
@@ -539,7 +539,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
     @Override
     public Object parse(ParsingEngine parsingEngine, ArgumentSource source, Class type, ArgumentMatches matches) {
         if(multiplexedIds == null)
-            throw new GATKException("Cannot directly parse a MultiplexArgumentTypeDescriptor; must create a derivative type descriptor first.");
+            throw new ReviewedStingException("Cannot directly parse a MultiplexArgumentTypeDescriptor; must create a derivative type descriptor first.");
 
         Map<Object,Object> multiplexedMapping = new HashMap<Object,Object>();
 
@@ -570,14 +570,14 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
                 if(!source.field.getName().equals(sourceField))
                     continue;
                 if(source.field.isAnnotationPresent(Multiplex.class))
-                    throw new GATKException("Command-line arguments can only depend on independent fields");
+                    throw new ReviewedStingException("Command-line arguments can only depend on independent fields");
                 sourceTypes[currentField] = source.field.getType();
                 sourceValues[currentField] = JVMUtils.getFieldValue(source.field,containingObject);
                 currentField++;
                 fieldFound = true;
             }
             if(!fieldFound)
-                throw new GATKException(String.format("Unable to find source field %s, referred to by dependent field %s",sourceField,dependentArgument.field.getName()));
+                throw new ReviewedStingException(String.format("Unable to find source field %s, referred to by dependent field %s",sourceField,dependentArgument.field.getName()));
         }
 
         Class<? extends Multiplexer> multiplexerType = dependentArgument.field.getAnnotation(Multiplex.class).value();
@@ -587,7 +587,7 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             multiplexerConstructor.setAccessible(true);
         }
         catch(NoSuchMethodException ex) {
-            throw new GATKException(String.format("Unable to find constructor for class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+            throw new ReviewedStingException(String.format("Unable to find constructor for class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
         }
 
         Multiplexer multiplexer = null;
@@ -595,13 +595,13 @@ class MultiplexArgumentTypeDescriptor extends ArgumentTypeDescriptor {
             multiplexer = multiplexerConstructor.newInstance(sourceValues);
         }
         catch(IllegalAccessException ex) {
-            throw new GATKException(String.format("Constructor for class %s with parameters %s is inaccessible",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+            throw new ReviewedStingException(String.format("Constructor for class %s with parameters %s is inaccessible",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
         }
         catch(InstantiationException ex) {
-            throw new GATKException(String.format("Can't create class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+            throw new ReviewedStingException(String.format("Can't create class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
         }
         catch(InvocationTargetException ex) {
-            throw new GATKException(String.format("Can't invoke constructor of class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
+            throw new ReviewedStingException(String.format("Can't invoke constructor of class %s with parameters %s",multiplexerType.getName(),Arrays.deepToString(sourceFields)),ex);
         }
 
         return new MultiplexArgumentTypeDescriptor(multiplexer,multiplexer.multiplex());
diff --git a/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java b/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
index 0fdeda438..9048cd200 100644
--- a/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
+++ b/java/src/org/broadinstitute/sting/commandline/CommandLineUtils.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 
@@ -123,7 +123,7 @@ public class CommandLineUtils {
         try {
             return annotation.getClass().getMethod(method).invoke(annotation);
         } catch (Exception e) {
-            throw new GATKException("Unable to access method " + method + " on annotation " + annotation.getClass(), e);
+            throw new ReviewedStingException("Unable to access method " + method + " on annotation " + annotation.getClass(), e);
         }
     }
 }
diff --git a/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java b/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
index 9b8e6ad23..261197ec8 100755
--- a/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
+++ b/java/src/org/broadinstitute/sting/commandline/ParsingEngine.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.commandline;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.Utils;
@@ -294,7 +294,7 @@ public class ParsingEngine {
         // Grab the first argument definition and report that one as the failure.  Theoretically, we should notify of all failures.
         List<ArgumentDefinition> definitions = argumentSource.createArgumentDefinitions();
         if(definitions.size() < 1)
-            throw new GATKException("Internal error.  Argument source creates no definitions.");
+            throw new ReviewedStingException("Internal error.  Argument source creates no definitions.");
         ArgumentDefinition definition = definitions.get(0);
         throw new UserException.DeprecatedArgument(definition.fullName,definition.doc);
     }
@@ -315,7 +315,7 @@ public class ParsingEngine {
 
         // Abort if no home is found for the object.
         if( targets.size() == 0 )
-            throw new GATKException("Internal command-line parser error: unable to find a home for argument matches " + argumentMatches);
+            throw new ReviewedStingException("Internal command-line parser error: unable to find a home for argument matches " + argumentMatches);
 
         for( Object target: targets ) {
             Object value = (argumentMatches.size() != 0) ? source.parse(this,argumentMatches) : source.createDefault();
diff --git a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
index 2bcc58aac..725bc3727 100755
--- a/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/GenomeAnalysisEngine.java
@@ -31,7 +31,7 @@ import net.sf.samtools.*;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
@@ -156,12 +156,12 @@ public class GenomeAnalysisEngine {
 
         // validate our parameters
         if (args == null) {
-            throw new GATKException("The GATKArgumentCollection passed to GenomeAnalysisEngine can not be null.");
+            throw new ReviewedStingException("The GATKArgumentCollection passed to GenomeAnalysisEngine can not be null.");
         }
 
         // validate our parameters              
         if (my_walker == null)
-            throw new GATKException("The walker passed to GenomeAnalysisEngine can not be null.");
+            throw new ReviewedStingException("The walker passed to GenomeAnalysisEngine can not be null.");
 
         // save our argument parameter
         this.argCollection = args;
@@ -808,7 +808,7 @@ public class GenomeAnalysisEngine {
                     drivingDataSource.getSequenceDictionary(),
                     SHARD_SIZE);
         } else
-            throw new GATKException("Unable to support walker of type" + walker.getClass().getName());
+            throw new ReviewedStingException("Unable to support walker of type" + walker.getClass().getName());
 
         return shardStrategy;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java b/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
index fdc2cb459..27a86ab3f 100755
--- a/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
+++ b/java/src/org/broadinstitute/sting/gatk/ReadMetrics.java
@@ -30,7 +30,7 @@ import java.util.Map;
 import java.util.HashMap;
 import java.util.Collections;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 /**
  * Holds a bunch of basic information about the traversal.
@@ -78,7 +78,7 @@ public class ReadMetrics implements Cloneable {
             newMetrics = (ReadMetrics)super.clone();
         }
         catch(CloneNotSupportedException ex) {
-            throw new GATKException("Unable to clone runtime metrics",ex);
+            throw new ReviewedStingException("Unable to clone runtime metrics",ex);
         }
         newMetrics.nRecords = nRecords;
         newMetrics.nReads = nReads;
diff --git a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
index 18bf662eb..45675092c 100755
--- a/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/WalkerManager.java
@@ -30,7 +30,7 @@ import org.broadinstitute.sting.commandline.Hidden;
 import org.broadinstitute.sting.gatk.filters.FilterManager;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.text.TextFormattingUtils;
 import org.broadinstitute.sting.utils.help.DescriptionTaglet;
@@ -168,7 +168,7 @@ public class WalkerManager extends PluginManager<Walker> {
     public static DataSource getWalkerDataSource(Class<? extends Walker> walkerClass) {
         By byDataSource = walkerClass.getAnnotation(By.class);
         if( byDataSource == null )
-            throw new GATKException("Unable to find By annotation for walker class " + walkerClass.getName());
+            throw new ReviewedStingException("Unable to find By annotation for walker class " + walkerClass.getName());
         return byDataSource.value();
     }
 
@@ -397,7 +397,7 @@ public class WalkerManager extends PluginManager<Walker> {
     private static Requires getWalkerRequirements(Class<? extends Walker> walkerClass) {
         Requires requiresDataSource = walkerClass.getAnnotation(Requires.class);
         if( requiresDataSource == null )
-            throw new GATKException( "Unable to find data types required by walker class " + walkerClass.getName());
+            throw new ReviewedStingException( "Unable to find data types required by walker class " + walkerClass.getName());
         return requiresDataSource;
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
index d80e95462..6abd8c209 100755
--- a/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
+++ b/java/src/org/broadinstitute/sting/gatk/arguments/GATKArgumentCollection.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.arguments;
 
 import net.sf.samtools.SAMFileReader;
 import org.broadinstitute.sting.gatk.phonehome.GATKRunReport;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Input;
@@ -191,7 +191,7 @@ public class GATKArgumentCollection {
         try {
             serializer.write(collection, result);
         } catch (Exception e) {
-            throw new GATKException("Failed to marshal the data to the file " + outputFile, e);
+            throw new ReviewedStingException("Failed to marshal the data to the file " + outputFile, e);
         }
     }
 
@@ -206,7 +206,7 @@ public class GATKArgumentCollection {
         try {
             serializer.write(collection, outputFile);
         } catch (Exception e) {
-            throw new GATKException("Failed to marshal the data to the file " + outputFile, e);
+            throw new ReviewedStingException("Failed to marshal the data to the file " + outputFile, e);
         }
     }
 
@@ -222,7 +222,7 @@ public class GATKArgumentCollection {
             GATKArgumentCollection example = serializer.read(GATKArgumentCollection.class, source);
             return example;
         } catch (Exception e) {
-            throw new GATKException("Failed to marshal the data from file " + filename, e);
+            throw new ReviewedStingException("Failed to marshal the data from file " + filename, e);
         }
     }
 
@@ -237,7 +237,7 @@ public class GATKArgumentCollection {
             GATKArgumentCollection example = serializer.read(GATKArgumentCollection.class, file);
             return example;
         } catch (Exception e) {
-            throw new GATKException("Failed to marshal the data from file " + file.toString(), e);
+            throw new ReviewedStingException("Failed to marshal the data from file " + file.toString(), e);
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
index 29867a7f4..255945619 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/AlignmentContext.java
@@ -26,7 +26,7 @@
 package org.broadinstitute.sting.gatk.contexts;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.ReadBackedExtendedEventPileup;
@@ -66,9 +66,9 @@ public class AlignmentContext {
     }
 
     public AlignmentContext(GenomeLoc loc, ReadBackedPileup basePileup, long skippedBases,boolean hasPileupBeenDownsampled ) {
-        if ( loc == null ) throw new GATKException("BUG: GenomeLoc in Alignment context is null");
-        if ( basePileup == null ) throw new GATKException("BUG: ReadBackedPileup in Alignment context is null");
-        if ( skippedBases < 0 ) throw new GATKException("BUG: skippedBases is -1 in Alignment context");
+        if ( loc == null ) throw new ReviewedStingException("BUG: GenomeLoc in Alignment context is null");
+        if ( basePileup == null ) throw new ReviewedStingException("BUG: ReadBackedPileup in Alignment context is null");
+        if ( skippedBases < 0 ) throw new ReviewedStingException("BUG: skippedBases is -1 in Alignment context");
 
         this.loc = loc;
         this.basePileup = basePileup;
@@ -89,7 +89,7 @@ public class AlignmentContext {
      */
     public ReadBackedPileup getBasePileup() {
         if(!hasBasePileup())
-            throw new GATKException("No base pileup is available.  Please check for a base pileup with hasBasePileup() before attempting to retrieve a pileup.");
+            throw new ReviewedStingException("No base pileup is available.  Please check for a base pileup with hasBasePileup() before attempting to retrieve a pileup.");
         return basePileup;
     }
 
@@ -99,7 +99,7 @@ public class AlignmentContext {
      */
     public ReadBackedExtendedEventPileup getExtendedEventPileup() {
         if(!hasExtendedEventPileup())
-            throw new GATKException("No extended event pileup is present.");
+            throw new ReviewedStingException("No extended event pileup is present.");
         return (ReadBackedExtendedEventPileup)basePileup; 
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
index 0221ef3db..96d49fc2e 100644
--- a/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/ReferenceContext.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.contexts;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.BaseUtils;
 import net.sf.samtools.util.StringUtil;
@@ -191,7 +191,7 @@ public class ReferenceContext {
         byte[] b = new byte[stop-start];
 
         if ( stop > bases.length )
-            throw new GATKException("Bases beyond the current window requested: window="+window+", requested="+n);
+            throw new ReviewedStingException("Bases beyond the current window requested: window="+window+", requested="+n);
 
         int i = 0;
         for ( int j = start ;  j < stop ; j++) b[i++]=bases[j];
diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java b/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java
index 2be1dea28..f42ab6a66 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/StratifiedAlignmentContext.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.contexts;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.*;
@@ -72,7 +72,7 @@ public class StratifiedAlignmentContext<RBP extends ReadBackedPileup> {
             case REVERSE:
                 return new AlignmentContext(loc,basePileup.getNegativeStrandPileup());
             default:
-                throw new GATKException("Unable to get alignment context for type = " + type);
+                throw new ReviewedStingException("Unable to get alignment context for type = " + type);
         }
     }
 
@@ -144,9 +144,9 @@ public class StratifiedAlignmentContext<RBP extends ReadBackedPileup> {
         boolean isExtended = contexts.iterator().next().basePileup instanceof ReadBackedExtendedEventPileup;
         for(StratifiedAlignmentContext context: contexts) {
             if(!loc.equals(context.getLocation()))
-                throw new GATKException("Illegal attempt to join contexts from different genomic locations");
+                throw new ReviewedStingException("Illegal attempt to join contexts from different genomic locations");
             if(isExtended != (context.basePileup instanceof ReadBackedExtendedEventPileup))
-                throw new GATKException("Illegal attempt to join simple and extended contexts");
+                throw new ReviewedStingException("Illegal attempt to join simple and extended contexts");
         }
 
         AlignmentContext jointContext;
diff --git a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
index eb037cf09..522366289 100755
--- a/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
@@ -30,7 +30,7 @@ import org.broad.tribble.util.popgen.HardyWeinbergCalculation;
 import org.broad.tribble.util.variantcontext.*;
 import org.broadinstitute.sting.utils.*;
 import org.broad.tribble.vcf.VCFConstants;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 public class VariantContextUtils {
@@ -111,7 +111,7 @@ public class VariantContextUtils {
      */
     public static List<JexlVCMatchExp> initializeMatchExps(String[] names, String[] exps) {
         if ( names == null || exps == null )
-            throw new GATKException("BUG: neither names nor exps can be null: names " + Arrays.toString(names) + " exps=" + Arrays.toString(exps) );
+            throw new ReviewedStingException("BUG: neither names nor exps can be null: names " + Arrays.toString(names) + " exps=" + Arrays.toString(exps) );
 
         if ( names.length != exps.length )
             throw new UserException("Inconsistent number of provided filter names and expressions: names=" + Arrays.toString(names) + " exps=" + Arrays.toString(exps));
@@ -323,7 +323,7 @@ public class VariantContextUtils {
 
         for ( VariantContext vc : VCs ) {
             if ( loc.getStart() != vc.getStart() ) // || !first.getReference().equals(vc.getReference()) )
-                throw new GATKException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString());
+                throw new ReviewedStingException("BUG: attempting to merge VariantContexts with different start sites: first="+ first.toString() + " second=" + vc.toString());
 
             if ( getLocation(vc).size() > loc.size() )
                 loc = getLocation(vc); // get the longest location
@@ -450,7 +450,7 @@ public class VariantContextUtils {
             if ( ref == null || ref.length() < myRef.length() )
                 ref = myRef;
             else if ( ref.length() == myRef.length() && ! ref.equals(myRef) )
-                throw new GATKException("BUG: equal length references with difference bases: "+ ref + " " + myRef);
+                throw new ReviewedStingException("BUG: equal length references with difference bases: "+ ref + " " + myRef);
         }
 
         return ref;
@@ -472,7 +472,7 @@ public class VariantContextUtils {
             //
 
             Allele myRef = vc.getReference();
-            if ( refAllele.length() <= myRef.length() ) throw new GATKException("BUG: myRef="+myRef+" is longer than refAllele="+refAllele);
+            if ( refAllele.length() <= myRef.length() ) throw new ReviewedStingException("BUG: myRef="+myRef+" is longer than refAllele="+refAllele);
             byte[] extraBases = Arrays.copyOfRange(refAllele.getBases(), myRef.length(), refAllele.length());
 
 //            System.out.printf("Remapping allele at %s%n", vc);
@@ -577,7 +577,7 @@ public class VariantContextUtils {
             padVC = false;
         else if (refAllele.length() == locLength-1)
             padVC = true;
-        else throw new GATKException("Badly formed variant context, reference length must be at most one base shorter than location size");
+        else throw new ReviewedStingException("Badly formed variant context, reference length must be at most one base shorter than location size");
 
 
         // nothing to do if we don't need to pad bases
@@ -591,7 +591,7 @@ public class VariantContextUtils {
             else if (attributes.containsKey(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY))
                 refByte = (Byte)attributes.get(VariantContext.REFERENCE_BASE_FOR_INDEL_KEY);
             else
-                throw new GATKException("Error when trying to pad Variant Context: either input reference base must be a regular base, or input VC must contain reference base key");
+                throw new ReviewedStingException("Error when trying to pad Variant Context: either input reference base must be a regular base, or input VC must contain reference base key");
 
             List<Allele> alleles = new ArrayList<Allele>();
             Map<String, Genotype> genotypes = new TreeMap<String, Genotype>();
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java b/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java
index d1c2b2b76..7e6cab6c8 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/DataSourceGenerationException.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 /**
  * User: aaron
@@ -20,7 +20,7 @@ import org.broadinstitute.sting.utils.exceptions.GATKException;
  * This exception is throw when we're unable to generate a data source,
  * most likely due to an incomplete input source list
  */
-public class DataSourceGenerationException extends GATKException {
+public class DataSourceGenerationException extends ReviewedStingException {
     public DataSourceGenerationException(String message) {
         super(message);
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
index 83fefe700..eff273d0e 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/LocusReferenceView.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.gatk.walkers.Walker;
@@ -85,8 +85,8 @@ public class LocusReferenceView extends ReferenceView {
         if( walker.getClass().isAnnotationPresent(Reference.class) ) {
             Window window = walker.getClass().getAnnotation(Reference.class).window();
 
-            if( window.start() > 0 ) throw new GATKException( "Reference window starts after current locus" );
-            if( window.stop() < 0 ) throw new GATKException( "Reference window ends before current locus" );
+            if( window.start() > 0 ) throw new ReviewedStingException( "Reference window starts after current locus" );
+            if( window.stop() < 0 ) throw new ReviewedStingException( "Reference window ends before current locus" );
 
             windowStart = window.start();
             windowStop = window.stop();
@@ -121,7 +121,7 @@ public class LocusReferenceView extends ReferenceView {
         if ( bounds==null || loc==null) return; // can bounds be null actually???
         if ( isLocationWithinBounds(loc) ) return;
         if ( loc.getContigIndex() != bounds.getContigIndex() )
-            throw new GATKException("Illegal attempt to expand reference view bounds to accommodate location on a different contig.");
+            throw new ReviewedStingException("Illegal attempt to expand reference view bounds to accommodate location on a different contig.");
 
         bounds = GenomeLocParser.createGenomeLoc(bounds.getContigIndex(),
                                                  Math.min(bounds.getStart(),loc.getStart()),
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
index ee4997164..385de4e5f 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ReferenceView.java
@@ -10,7 +10,7 @@ import net.sf.samtools.SAMSequenceRecord;
 import net.sf.samtools.SAMRecord;
 import net.sf.picard.reference.ReferenceSequence;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 /**
  * User: hanna
  * Date: May 22, 2009
@@ -80,7 +80,7 @@ public class ReferenceView implements View {
         int overhang = (int)(genomeLoc.getStop() - stop);
         if ( overhang > 0 ) {
             if ( overhang > BUFFER ) // todo -- this is a bit dangerous
-                throw new GATKException("Insufficient buffer size for Xs overhanging genome -- expand BUFFER");
+                throw new ReviewedStingException("Insufficient buffer size for Xs overhanging genome -- expand BUFFER");
             byte[] all = new byte[subsequence.getBases().length + overhang];
             System.arraycopy(subsequence.getBases(), 0, all, 0, subsequence.getBases().length);
             System.arraycopy(Xs, 0, all, subsequence.getBases().length, overhang);
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
index f4ca0b05c..cb912ccf9 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProvider.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.providers;
 
 import org.broadinstitute.sting.gatk.datasources.shards.Shard;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -110,7 +110,7 @@ public abstract class ShardDataProvider {
             Collection<Class<? extends View>> conflicts = registeredView.getConflictingViews();
             for( Class<? extends View> conflict: conflicts ) {
                 if( conflict.isInstance(view) )
-                    throw new GATKException(String.format("Tried to register two conflicting views: %s and %s",
+                    throw new ReviewedStingException(String.format("Tried to register two conflicting views: %s and %s",
                                                            registeredView.getClass().getSimpleName(),
                                                            view.getClass().getSimpleName()));
             }
@@ -120,7 +120,7 @@ public abstract class ShardDataProvider {
         for( Class<? extends View> conflict: view.getConflictingViews() ) {
             for( View registeredView: registeredViews ) {
                 if( conflict.isInstance(registeredView) )
-                    throw new GATKException(String.format("Tried to register two conflicting views: %s and %s",
+                    throw new ReviewedStingException(String.format("Tried to register two conflicting views: %s and %s",
                                                            registeredView.getClass().getSimpleName(),
                                                            view.getClass().getSimpleName()));
             }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
index 5f9bdb958..0c4c08480 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/IntervalSharder.java
@@ -35,7 +35,7 @@ import java.util.*;
 
 import net.sf.samtools.*;
 import net.sf.picard.util.PeekableIterator;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 /**
  * Shard intervals based on position within the BAM file.
@@ -124,7 +124,7 @@ public class IntervalSharder {
 
         for(GenomeLoc location: loci) {
             if(!location.getContig().equals(contig))
-                throw new GATKException("Location outside bounds of contig");
+                throw new ReviewedStingException("Location outside bounds of contig");
 
             if(!binIterator.hasNext())
                 break;
@@ -191,7 +191,7 @@ public class IntervalSharder {
                 }
                 else {
                     if(lastFilePointer == null)
-                        throw new GATKException("Illegal state: initializer failed to create cached file pointer.");
+                        throw new ReviewedStingException("Illegal state: initializer failed to create cached file pointer.");
 
                     // The start of the region overlaps the bin.  Add the overlapping subset.
                     final int regionStop = Math.min(locationStop,binStop);
@@ -475,7 +475,7 @@ class BinQueueState implements Comparable<BinQueueState> {
         // Both BinQueueStates have next bins.  Before proceeding, make sure the bin cache is valid.
         if(this.firstLocusInCurrentBin <= 0 || this.lastLocusInCurrentBin <= 0 ||
            other.firstLocusInCurrentBin <= 0 || other.lastLocusInCurrentBin <= 0) {
-            throw new GATKException("Sharding mechanism error - bin->locus cache is invalid.");
+            throw new ReviewedStingException("Sharding mechanism error - bin->locus cache is invalid.");
         }
 
         // Straight integer subtraction works here because lhsStart, rhsStart always positive.
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
index 2af2caf68..98df7b7b1 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/MonolithicShard.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.shards;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.gatk.ReadMetrics;
 import org.broadinstitute.sting.gatk.ReadProperties;
@@ -42,7 +42,7 @@ public class MonolithicShard implements Shard {
     public MonolithicShard(SAMDataSource readsDataSource, ShardType shardType, List<GenomeLoc> locs) {
         this.readsDataSource = readsDataSource;
         if(shardType != ShardType.LOCUS && shardType != ShardType.READ)
-            throw new GATKException("Invalid shard type for monolithic shard: " + shardType);
+            throw new ReviewedStingException("Invalid shard type for monolithic shard: " + shardType);
         this.shardType = shardType;
         this.locs = locs;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java
index 74ee8361e..2bc7a3207 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/shards/ShardStrategyFactory.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.shards;
 
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource;
 
@@ -71,7 +71,7 @@ public class ShardStrategyFactory {
             case READS_EXPERIMENTAL:
                 return new ReadShardStrategy(readsDataSource,null);
             default:
-                throw new GATKException("Strategy: " + strat + " isn't implemented for this type of shatter request");
+                throw new ReviewedStingException("Strategy: " + strat + " isn't implemented for this type of shatter request");
         }
 
     }
@@ -109,7 +109,7 @@ public class ShardStrategyFactory {
             case READS_EXPERIMENTAL:
                 return new ReadShardStrategy(readsDataSource,lst);
             default:
-                throw new GATKException("Strategy: " + strat + " isn't implemented");
+                throw new ReviewedStingException("Strategy: " + strat + " isn't implemented");
         }
 
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java
index 83d4ad469..825131962 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceDataSource.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import net.sf.picard.reference.FastaSequenceIndexBuilder;
 import net.sf.picard.sam.CreateSequenceDictionary;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
@@ -68,7 +68,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
             try {
                 // get exclusive lock
                 if (!indexLock.exclusiveLock())
-                    throw new GATKException("Index file could not be written because a lock could not be obtained." +
+                    throw new ReviewedStingException("Index file could not be written because a lock could not be obtained." +
                             "If you are running multiple instances of GATK, another process is probably creating this " +
                             "file now. Please wait until it is finished and try again.");
                 FastaSequenceIndexBuilder faiBuilder = new FastaSequenceIndexBuilder(fastaFile, this);
@@ -82,7 +82,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
             catch (Exception e) {
                 // If lock creation succeeded, the failure must have been generating the index.
                 // If lock creation failed, just skip over index creation entirely.
-                throw new GATKException("Index file does not exist and could not be created because " + e.getMessage(), e);
+                throw new ReviewedStingException("Index file does not exist and could not be created because " + e.getMessage(), e);
             }
             finally {
                 indexLock.unlock();
@@ -108,7 +108,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
             try {
                 // get shared lock on dict file so nobody else can start creating it
                 if (!dictLock.exclusiveLock())
-                    throw new GATKException("Dictionary file could not be written because a lock could not be obtained." +
+                    throw new ReviewedStingException("Dictionary file could not be written because a lock could not be obtained." +
                             "If you are running multiple instances of GATK, another process is probably creating this " +
                             "file now. Please wait until it is finished and try again.");
                 // dict will be written to random temporary file in same directory (see note above)
@@ -121,7 +121,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
                 new CreateSequenceDictionary().instanceMain(args);
 
                 if (!tempFile.renameTo(dictFile))
-                    throw new GATKException("Error transferring temp file " + tempFile + " to dict file " + dictFile);
+                    throw new ReviewedStingException("Error transferring temp file " + tempFile + " to dict file " + dictFile);
             }
             catch(FileSystemInabilityToLockException ex) {
                 logger.info("Unable to create write lock: " + ex.getMessage());
@@ -130,7 +130,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
             catch (Exception e) {
                 // If lock creation succeeded, the failure must have been generating the index.
                 // If lock creation failed, just skip over index creation entirely.
-                throw new GATKException("Dictionary file does not exist and could not be created because " + e.getMessage(), e);
+                throw new ReviewedStingException("Dictionary file does not exist and could not be created because " + e.getMessage(), e);
             }
             finally {
                 dictLock.unlock();
@@ -149,7 +149,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
         try {
             try {
                 if (!dictLock.sharedLock()) {
-                    throw new GATKException("Could not open dictionary file because a lock could not be obtained.");
+                    throw new ReviewedStingException("Could not open dictionary file because a lock could not be obtained.");
                 }
             }
             catch(FileSystemInabilityToLockException ex) {
@@ -159,7 +159,7 @@ public class ReferenceDataSource implements ReferenceDataSourceProgressListener
 
             try {
                 if (!indexLock.sharedLock()) {
-                    throw new GATKException("Could not open index file because a lock could not be obtained.");
+                    throw new ReviewedStingException("Could not open index file because a lock could not be obtained.");
                 }
             }
             catch(FileSystemInabilityToLockException ex) {
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java
index 1aaee0bb2..f67ed96f6 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ReferenceOrderedDataSource.java
@@ -11,7 +11,7 @@ import org.broadinstitute.sting.gatk.refdata.utils.FlashBackIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
@@ -156,7 +156,7 @@ class ReferenceOrderedDataPool extends ResourcePool<LocationAwareSeekableRODIter
             return null;
         }
         else {
-            throw new GATKException("Unable to find a ROD iterator for segments of type " + segment.getClass());
+            throw new ReviewedStingException("Unable to find a ROD iterator for segments of type " + segment.getClass());
         }
     }
 
@@ -215,7 +215,7 @@ class ReferenceOrderedQueryDataPool extends ResourcePool<FeatureSource, Location
                 return new SeekableRODIterator(new FeatureToGATKFeatureIterator(resource.iterator(),rod.getName()));
             }
         } catch (IOException e) {
-            throw new GATKException("Unable to create iterator for rod named " + rod.getName(),e);
+            throw new ReviewedStingException("Unable to create iterator for rod named " + rod.getName(),e);
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java
index 862c58617..cdf03807a 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/ResourcePool.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
@@ -88,10 +88,10 @@ abstract class ResourcePool <T,I extends Iterator> {
 
             // make sure we actually removed the assignment
             if (obj == null)
-                    throw new GATKException("Failed to remove resource assignment; target key had no associated value in the resource assignment map");
+                    throw new ReviewedStingException("Failed to remove resource assignment; target key had no associated value in the resource assignment map");
             // Return the resource to the pool.
             if( !allResources.contains(resource) )
-                throw new GATKException("Iterator does not belong to the given pool.");
+                throw new ReviewedStingException("Iterator does not belong to the given pool.");
             availableResources.add(resource);
         }
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
index 69d43b92a..149468cb5 100755
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SAMDataSource.java
@@ -41,7 +41,7 @@ import org.broadinstitute.sting.gatk.ReadProperties;
 import org.broadinstitute.sting.gatk.ReadMetrics;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.gatk.filters.CountingFilteringIterator;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
@@ -294,7 +294,7 @@ public class SAMDataSource implements SimpleDataSource {
      */
     public void fillShard(BAMFormatAwareShard shard) {
         if(!shard.buffersReads())
-            throw new GATKException("Attempting to fill a non-buffering shard.");
+            throw new ReviewedStingException("Attempting to fill a non-buffering shard.");
 
         SAMReaders readers = resourcePool.getAvailableReaders();
         // Cache the most recently viewed read so that we can check whether we've reached the end of a pair.
@@ -326,7 +326,7 @@ public class SAMDataSource implements SimpleDataSource {
             return seekMonolithic(shard);
 
         if(!(shard instanceof BAMFormatAwareShard))
-            throw new GATKException("BlockDrivenSAMDataSource cannot operate on shards of type: " + shard.getClass());
+            throw new ReviewedStingException("BlockDrivenSAMDataSource cannot operate on shards of type: " + shard.getClass());
         BAMFormatAwareShard bamAwareShard = (BAMFormatAwareShard)shard;
 
         if(bamAwareShard.buffersReads()) {
@@ -349,7 +349,7 @@ public class SAMDataSource implements SimpleDataSource {
             if(readers.getReader(id) == read.getFileSource().getReader())
                 return id;
         }
-        throw new GATKException("Unable to find id for reader associated with read " + read.getReadName());
+        throw new ReviewedStingException("Unable to find id for reader associated with read " + read.getReadName());
     }
 
     /**
@@ -508,7 +508,7 @@ public class SAMDataSource implements SimpleDataSource {
 
         public synchronized void releaseReaders(SAMReaders readers) {
             if(!allResources.contains(readers))
-                throw new GATKException("Tried to return readers from the pool that didn't originate in the pool.");
+                throw new ReviewedStingException("Tried to return readers from the pool that didn't originate in the pool.");
             availableResources.add(readers);
         }
 
@@ -523,12 +523,12 @@ public class SAMDataSource implements SimpleDataSource {
                 if(id != null)
                     return id;
             }
-            throw new GATKException("No such reader id is available");
+            throw new ReviewedStingException("No such reader id is available");
         }
 
         private synchronized void createNewResource() {
             if(allResources.size() > maxEntries)
-                throw new GATKException("Cannot create a new resource pool.  All resources are in use.");
+                throw new ReviewedStingException("Cannot create a new resource pool.  All resources are in use.");
             SAMReaders readers = new SAMReaders(readProperties);
             allResources.add(readers);
             availableResources.add(readers);
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java
index 7dc2b51fa..e890e6d3a 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceLoadException.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 /**
  *
@@ -28,7 +28,7 @@ import org.broadinstitute.sting.utils.exceptions.GATKException;
  * <p/>
  * Generate this on a simple data source load exception
  */
-public class SimpleDataSourceLoadException extends GATKException {
+public class SimpleDataSourceLoadException extends ReviewedStingException {
     public SimpleDataSourceLoadException(String msg) {
         super(msg);
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java
index 040327bc3..d83bb4ce9 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/simpleDataSources/SimpleDataSourceSplitException.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.datasources.simpleDataSources;
 
 
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 
 /*
@@ -39,7 +39,7 @@ import org.broadinstitute.sting.utils.exceptions.GATKException;
  * <p/>
  * an exception that get's thrown if we can't split up a data source appropriately
  */
-public class SimpleDataSourceSplitException extends GATKException {
+public class SimpleDataSourceSplitException extends ReviewedStingException {
     public SimpleDataSourceSplitException(String msg) {
         super(msg);
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java b/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java
index 1cadb1252..327c747f3 100644
--- a/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java
+++ b/java/src/org/broadinstitute/sting/gatk/datasources/utilities/BAMFileStat.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.gatk.datasources.utilities;
 
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.instrumentation.Sizeof;
 
 import java.io.File;
@@ -58,7 +58,7 @@ public class BAMFileStat extends CommandLineProgram {
     public int execute() {
         switch(command) {
             case ShowBlocks:
-                throw new GATKException("The BAM block inspector has been disabled.");
+                throw new ReviewedStingException("The BAM block inspector has been disabled.");
             case ShowIndex:
                 showIndexBins(new File(bamFileName),range);
                 break;
@@ -171,7 +171,7 @@ public class BAMFileStat extends CommandLineProgram {
             }
         }
         catch(IllegalAccessException ex) {
-            throw new GATKException("Unable to examine cached index",ex);
+            throw new ReviewedStingException("Unable to examine cached index",ex);
         }
 
         System.out.printf("%nOverall: %d bins, %d chunks, %d linear index entries",numBins,numChunks,numLinearIndexEntries);
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
index 6d2a25565..3cdcaddcf 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/Accumulator.java
@@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.datasources.providers.ShardDataProvider;
 import org.broadinstitute.sting.gatk.datasources.providers.LocusShardDataProvider;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.GenomeLocSortedSet;
@@ -184,7 +184,7 @@ public abstract class Accumulator {
          */
         public void accumulate( ShardDataProvider provider, Object result ) {
             if(!(provider instanceof LocusShardDataProvider))
-                throw new GATKException("Unable to reduce by interval on reads traversals at this time.");
+                throw new ReviewedStingException("Unable to reduce by interval on reads traversals at this time.");
 
             GenomeLoc location = ((LocusShardDataProvider)provider).getLocus();
 
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
index 477d522a1..feae86587 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/HierarchicalMicroScheduler.java
@@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.SAMDataSource
 import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
 import org.broadinstitute.sting.gatk.io.*;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.threading.ThreadPoolMonitor;
 
 import javax.management.MBeanServer;
@@ -109,7 +109,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
             mbs.registerMBean(this, name);
         }
         catch (JMException ex) {
-            throw new GATKException("Unable to register microscheduler with JMX", ex);
+            throw new ReviewedStingException("Unable to register microscheduler with JMX", ex);
         }
     }
 
@@ -129,7 +129,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
         while (isShardTraversePending() || isTreeReducePending()) {
             // Check for errors during execution.
             if(hasTraversalErrorOccurred())
-                throw new GATKException("An error has occurred during the traversal.",getTraversalError());
+                throw new ReviewedStingException("An error has occurred during the traversal.",getTraversalError());
 
             // Too many files sitting around taking up space?  Merge them.
             if (isMergeLimitExceeded())
@@ -158,7 +158,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
             notifyTraversalDone(walker,result);
         }
         catch (Exception ex) {
-            throw new GATKException("Unable to retrieve result", ex);
+            throw new ReviewedStingException("Unable to retrieve result", ex);
         }
 
         outputTracker.close();
@@ -358,7 +358,7 @@ public class HierarchicalMicroScheduler extends MicroScheduler implements Hierar
 
     private synchronized Throwable getTraversalError() {
         if(!hasTraversalErrorOccurred())
-            throw new GATKException("User has attempted to retrieve a traversal error when none exists");
+            throw new ReviewedStingException("User has attempted to retrieve a traversal error when none exists");
         return error;
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
index 661a99fd6..62788737c 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/ShardTraverser.java
@@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.traversals.TraversalEngine;
 import org.broadinstitute.sting.gatk.io.ThreadLocalOutputTracker;
 import org.broadinstitute.sting.gatk.walkers.Walker;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.concurrent.Callable;
 /**
@@ -83,7 +83,7 @@ public class ShardTraverser implements Callable {
         catch(Throwable t) {
             // Notify that an exception has occurred and rethrow it.
             microScheduler.notifyOfTraversalError(t);
-            throw new GATKException("An error has occurred during traversal",t);
+            throw new ReviewedStingException("An error has occurred during traversal",t);
         }
         finally {
             synchronized(this) {
@@ -115,7 +115,7 @@ public class ShardTraverser implements Callable {
             }
         }
         catch( InterruptedException ex ) {
-            throw new GATKException("Interrupted while waiting for more output to be finalized.",ex);
+            throw new ReviewedStingException("Interrupted while waiting for more output to be finalized.",ex);
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java b/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
index 8485eafd5..8fb4adb5d 100755
--- a/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
+++ b/java/src/org/broadinstitute/sting/gatk/executive/TreeReducer.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.executive;
 
 import org.broadinstitute.sting.gatk.walkers.TreeReducible;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.concurrent.Callable;
 import java.util.concurrent.Future;
@@ -90,11 +90,11 @@ public class TreeReducer implements Callable {
         }
         catch( InterruptedException ex ) {
             microScheduler.notifyOfTraversalError(ex);
-            throw new GATKException("Hierarchical reduce interrupted", ex);
+            throw new ReviewedStingException("Hierarchical reduce interrupted", ex);
         }
         catch( ExecutionException ex ) {
             microScheduler.notifyOfTraversalError(ex);
-            throw new GATKException("Hierarchical reduce failed", ex);
+            throw new ReviewedStingException("Hierarchical reduce failed", ex);
         }
 
         long endTime = System.currentTimeMillis();
diff --git a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
index 92bf8327b..5acf579e7 100755
--- a/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/OutputTracker.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.io;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.commandline.ArgumentSource;
 import org.broadinstitute.sting.utils.sam.SAMFileReaderBuilder;
@@ -139,7 +139,7 @@ public abstract class OutputTracker {
      */
     protected <T> T getTargetStream( Stub<T> stub ) {
         if( !outputs.containsKey(stub) )
-            throw new GATKException("OutputTracker was not notified that this stub exists: " + stub);
+            throw new ReviewedStingException("OutputTracker was not notified that this stub exists: " + stub);
         Storage<T> storage = outputs.get(stub);
         if( storage == null ) {
             storage = StorageFactory.createStorage(stub);
diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
index 541a46b3b..4dc976289 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/OutputStreamStorage.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.io.storage;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
@@ -59,7 +59,7 @@ public class OutputStreamStorage extends OutputStream implements Storage<OutputS
             this.outputStream = stub.getOutputStream();           
         }
         else
-            throw new GATKException("Not enough information to create storage for an OutputStream; need either a file or an existing output stream");
+            throw new ReviewedStingException("Not enough information to create storage for an OutputStream; need either a file or an existing output stream");
     }
 
     public OutputStreamStorage( OutputStreamStub stub, File file ) {
diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java b/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
index ffd9b8c83..ee5c56524 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/StorageFactory.java
@@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.io.stubs.Stub;
 import org.broadinstitute.sting.gatk.io.stubs.OutputStreamStub;
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterStub;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 
@@ -85,7 +85,7 @@ public class StorageFactory {
                 storage = new VCFWriterStorage(vcfWriterStub);
         }
         else
-            throw new GATKException("Unsupported stub type: " + stub.getClass().getName());
+            throw new ReviewedStingException("Unsupported stub type: " + stub.getClass().getName());
 
         return storage;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
index 539d74890..ac8740289 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/storage/VCFWriterStorage.java
@@ -5,7 +5,7 @@ import org.broad.tribble.vcf.VCFHeader;
 import org.broad.tribble.vcf.VCFHeaderLine;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.VCFWriter;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.gatk.io.stubs.VCFWriterStub;
 
 import java.io.*;
@@ -48,7 +48,7 @@ public class VCFWriterStorage implements Storage<VCFWriterStorage>, VCFWriter {
             this.stream = stub.getOutputStream();
         }
         else
-            throw new GATKException("Unable to create target to which to write; storage was provided with neither a file nor a stream.");
+            throw new ReviewedStingException("Unable to create target to which to write; storage was provided with neither a file nor a stream.");
 
         writer = new StandardVCFWriter(stream);
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
index 2b5cc7917..ca73ac29d 100644
--- a/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
+++ b/java/src/org/broadinstitute/sting/gatk/io/stubs/SAMFileWriterStub.java
@@ -35,7 +35,7 @@ import java.io.OutputStream;
 import org.broadinstitute.sting.gatk.io.OutputTracker;
 import org.broadinstitute.sting.gatk.io.StingSAMFileWriter;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 /**
@@ -156,7 +156,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     public void setCompressionLevel( Integer compressionLevel ) {
         if(writeStarted)
-            throw new GATKException("Attempted to change the compression level of a file with alignments already in it.");
+            throw new ReviewedStingException("Attempted to change the compression level of a file with alignments already in it.");
         this.compressionLevel = compressionLevel;
     }
 
@@ -192,7 +192,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     public void setPresorted(boolean presorted) {
         if(writeStarted)
-            throw new GATKException("Attempted to change the presorted state of a file with alignments already in it.");
+            throw new ReviewedStingException("Attempted to change the presorted state of a file with alignments already in it.");
         this.presorted = presorted;
     }
 
@@ -210,7 +210,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     public void setMaxRecordsInRam(int maxRecordsInRam) {
         if(writeStarted)
-            throw new GATKException("Attempted to change the max records in RAM of a file with alignments already in it.");
+            throw new ReviewedStingException("Attempted to change the max records in RAM of a file with alignments already in it.");
         this.maxRecordsInRam = maxRecordsInRam;
     }
 
@@ -228,7 +228,7 @@ public class SAMFileWriterStub implements Stub<SAMFileWriter>, StingSAMFileWrite
      */
     public void writeHeader(SAMFileHeader header) {
         if(writeStarted)
-            throw new GATKException("Attempted to change the header of a file with alignments already in it.");
+            throw new ReviewedStingException("Attempted to change the header of a file with alignments already in it.");
         this.headerOverride = header;
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java b/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
index f913f9464..f3a060be1 100644
--- a/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/iterators/BufferingReadIterator.java
@@ -31,7 +31,7 @@ import java.util.Queue;
 import java.util.LinkedList;
 import java.util.NoSuchElementException;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 /**
  * Buffers access to a large stream of reads, replenishing the buffer only when the reads  
@@ -66,7 +66,7 @@ public class BufferingReadIterator implements CloseableIterator<SAMRecord> {
     }
 
     public void remove() {
-        throw new GATKException("Unable to remove from a BufferingReadIterator");
+        throw new ReviewedStingException("Unable to remove from a BufferingReadIterator");
     }
 
     /**
diff --git a/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java b/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
index 6cab3a353..9d67fdf05 100644
--- a/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
+++ b/java/src/org/broadinstitute/sting/gatk/phonehome/GATKRunReport.java
@@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.CommandLineGATK;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.GATKArgumentCollection;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.simpleframework.xml.Element;
 import org.simpleframework.xml.ElementList;
@@ -169,7 +169,7 @@ public class GATKRunReport {
      */
     public GATKRunReport(Walker<?,?> walker, Exception e, GenomeAnalysisEngine engine, PhoneHomeOption type) {
         if ( type == PhoneHomeOption.NO_ET )
-            throw new GATKException("Trying to create a run report when type is NO_ET!");
+            throw new ReviewedStingException("Trying to create a run report when type is NO_ET!");
 
         mGATKHeader = CommandLineGATK.createApplicationHeader();
         currentPath = System.getProperty("user.dir");
@@ -245,7 +245,7 @@ public class GATKRunReport {
             serializer.write(this, stream);
             //throw new StingException("test");
         } catch (Exception e) {
-            throw new GATKException("Failed to marshal the data to the file " + stream, e);
+            throw new ReviewedStingException("Failed to marshal the data to the file " + stream, e);
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java b/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java
index 0b1c41857..63ee1a62b 100755
--- a/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/IntervalRod.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.refdata;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.io.File;
@@ -28,7 +28,7 @@ public class IntervalRod extends BasicReferenceOrderedDatum {
 	}
 
 	public String repl() {
-		throw new GATKException("repl() is not implemented yet");
+		throw new ReviewedStingException("repl() is not implemented yet");
 	}
 
 	public String toSimpleString() { return loc.toString(); }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java b/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java
index 215c09f55..3b879b232 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/PlinkRod.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.refdata;
 
 import org.broad.tribble.util.variantcontext.Allele;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
@@ -65,7 +65,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
         try {
             plink.initialize(file);
         } catch (FileNotFoundException e) {
-            throw new GATKException("Unable to find file " + file);
+            throw new ReviewedStingException("Unable to find file " + file);
         }
         return plink;
     }
@@ -188,9 +188,9 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
             return seqVars;
 
         } catch ( FileNotFoundException e ) {
-            throw new GATKException("File "+file.getAbsolutePath()+" could not be found. This was checked earlier. Should never happen.",e);
+            throw new ReviewedStingException("File "+file.getAbsolutePath()+" could not be found. This was checked earlier. Should never happen.",e);
         } catch ( IOException e ) {
-            throw new GATKException("Error reading file "+file.getAbsolutePath()+".",e);
+            throw new ReviewedStingException("Error reading file "+file.getAbsolutePath()+".",e);
         }
     }
 
@@ -200,7 +200,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
         }
 
         if ( plinkFileType != PlinkFileType.STANDARD_PED )
-            throw new GATKException("Plink file is likely of .raw or recoded format. Please use an uncoded .ped file.");
+            throw new ReviewedStingException("Plink file is likely of .raw or recoded format. Please use an uncoded .ped file.");
 
         StringTokenizer st = new StringTokenizer(plinkLine, "\t");
         int offset = 0;
@@ -224,7 +224,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
         // if the first line is not a comment (what we're used to seeing),
         // then it's the raw header (comes from de-binary-ing a .bed file)
         if ( !header.startsWith("#") )
-            throw new GATKException("Plink file is likely of .raw or recoded format. Please use an uncoded .ped file.");
+            throw new ReviewedStingException("Plink file is likely of .raw or recoded format. Please use an uncoded .ped file.");
 
         plinkFileType = PlinkFileType.STANDARD_PED;
 
@@ -281,7 +281,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
         try {
             reader = new BufferedReader( new FileReader( bimFile ));
         } catch ( FileNotFoundException e) {
-            throw new GATKException("The SNP information file accompanying the binary ped file was not found (the .bim file). "+
+            throw new ReviewedStingException("The SNP information file accompanying the binary ped file was not found (the .bim file). "+
                                      "Please ensure that it is in the same directory as the .bed and .fam files. The file we "+
                                      "Were looking for was "+bimFile.getAbsolutePath(),e);
         }
@@ -300,7 +300,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
                 line = reader.readLine();
             }
         } catch ( IOException e ) {
-            throw new GATKException("There was an error reading the .bim file "+bimFile.getAbsolutePath(), e);
+            throw new ReviewedStingException("There was an error reading the .bim file "+bimFile.getAbsolutePath(), e);
         }
 
         return variants;
@@ -311,7 +311,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
         try {
             reader = new BufferedReader( new FileReader( famFile ));
         } catch ( FileNotFoundException e) {
-            throw new GATKException("The Family information file accompanying the binary ped file was not found (the .fam file). "+
+            throw new ReviewedStingException("The Family information file accompanying the binary ped file was not found (the .fam file). "+
                                      "Please ensure that it is in the same directory as the .bed and .bim files. The file we "+
                                      "Were looking for was "+famFile.getAbsolutePath(),e);
         }
@@ -327,7 +327,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
                 }
             } while ( line != null );
         } catch (IOException e) {
-            throw new GATKException("There was an error reading the .fam file "+famFile.getAbsolutePath(),e);
+            throw new ReviewedStingException("There was an error reading the .fam file "+famFile.getAbsolutePath(),e);
         }
 
         return sampleNames;
@@ -338,7 +338,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
         try {
             inStream = new FileInputStream(bedFile);
         } catch (FileNotFoundException e) {
-            throw new GATKException("The Binary pedigree file file accompanying the family file was not found (the .bed file). "+
+            throw new ReviewedStingException("The Binary pedigree file file accompanying the family file was not found (the .bed file). "+
                                      "Please ensure that it is in the same directory as the .bim and .fam files. The file we "+
                                      "Were looking for was "+bedFile.getAbsolutePath(),e);
         }
@@ -378,7 +378,7 @@ public class PlinkRod extends BasicReferenceOrderedDatum implements Iterator<Pli
                 }
             } while ( genotype != -1 );
         } catch ( IOException e) {
-            throw new GATKException("Error reading binary ped file "+bedFile.getAbsolutePath(), e);
+            throw new ReviewedStingException("Error reading binary ped file "+bedFile.getAbsolutePath(), e);
         }
 
         return variants;
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java
index 5f7bd10f8..fa0c323b5 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordIterator.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.refdata;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.text.XReadLines;
@@ -123,7 +123,7 @@ public class RODRecordIterator<ROD extends ReferenceOrderedDatum> implements Ite
             named_constructor = type.getConstructor(String.class);
         }
         catch (java.lang.NoSuchMethodException e) {
-            throw new GATKException("ROD class "+type.getName()+" does not have constructor that accepts a single String argument (track name)");
+            throw new ReviewedStingException("ROD class "+type.getName()+" does not have constructor that accepts a single String argument (track name)");
         }
         ROD rod = instantiateROD(name);
         fieldDelimiter = rod.delimiterRegex(); // get delimiter from the ROD itself
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
index e5f0487d5..3a7b26753 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RODRecordListImpl.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.gatk.refdata;
 
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.util.*;
@@ -47,10 +47,10 @@ public class RODRecordListImpl extends AbstractList<GATKFeature> implements Comp
             records.add(r);
             if ( r == null ) continue;
             if ( ! this.name.equals(r.getName() ) ) {
-                throw new GATKException("Attempt to add GATKFeature with non-matching name "+r.getName()+" to the track "+name);
+                throw new ReviewedStingException("Attempt to add GATKFeature with non-matching name "+r.getName()+" to the track "+name);
             }
             if ( location != null && ! location.overlapsP(r.getLocation()) ) {
-                    throw new GATKException("Attempt to add GATKFeature that lies outside of specified interval "+location+"; offending GATKFeature:\n"+r.toString());
+                    throw new ReviewedStingException("Attempt to add GATKFeature that lies outside of specified interval "+location+"; offending GATKFeature:\n"+r.toString());
             }
         }
     }
@@ -72,7 +72,7 @@ public class RODRecordListImpl extends AbstractList<GATKFeature> implements Comp
     public void add(GATKFeature record, boolean allowNameMismatch) {
         if ( record != null ) {
             if ( ! allowNameMismatch && ! name.equals(record.getName() ) )
-                throw new GATKException("Attempt to add GATKFeature with non-matching name "+record.getName()+" to the track "+name);
+                throw new ReviewedStingException("Attempt to add GATKFeature with non-matching name "+record.getName()+" to the track "+name);
         }
         records.add(record);
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
index a9d82a112..6bb6d19dc 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/RefMetaDataTracker.java
@@ -5,7 +5,7 @@ import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
@@ -290,7 +290,7 @@ public class RefMetaDataTracker {
         Collection<VariantContext> contexts = getVariantContexts(ref, name, allowedTypes, curLocation, requireStartHere, false );
 
         if ( contexts.size() > 1 )
-            throw new GATKException("Requested a single VariantContext object for track " + name + " but multiple variants were present at position " + curLocation);
+            throw new ReviewedStingException("Requested a single VariantContext object for track " + name + " but multiple variants were present at position " + curLocation);
         else if ( contexts.size() == 0 )
             return null;
         else
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java b/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
index f0180a4be..c995f53bc 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/SeekableRODIterator.java
@@ -5,7 +5,7 @@ import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -131,7 +131,7 @@ public class SeekableRODIterator implements LocationAwareSeekableRODIterator {
      */
      public RODRecordList next() {
          if ( ! next_is_allowed )
-             throw new GATKException("Illegal use of iterator: Can not advance iterator with next() after seek-forward query of length > 1");
+             throw new ReviewedStingException("Illegal use of iterator: Can not advance iterator with next() after seek-forward query of length > 1");
 
          curr_position++;
  //        curr_query_end = -1;
@@ -178,7 +178,7 @@ public class SeekableRODIterator implements LocationAwareSeekableRODIterator {
              r = it.next(); // we got here only if we do need next record, time to load it for real
 
              long stop = r.getLocation().getStop();
-             if ( stop < curr_position ) throw new GATKException("DEBUG: encountered contig that should have been loaded earlier"); // this should never happen
+             if ( stop < curr_position ) throw new ReviewedStingException("DEBUG: encountered contig that should have been loaded earlier"); // this should never happen
              if ( stop > max_position ) max_position = stop; // max_position keeps the rightmost stop position across all loaded records
              records.add(r);
          }
@@ -257,14 +257,14 @@ public class SeekableRODIterator implements LocationAwareSeekableRODIterator {
     public RODRecordList seekForward(GenomeLoc interval) {
 
         if ( interval.getContigIndex() < curr_contig )
-            throw new GATKException("Out of order query: query contig "+interval.getContig()+" is located before "+
+            throw new ReviewedStingException("Out of order query: query contig "+interval.getContig()+" is located before "+
                                      "the iterator's current contig");
         if ( interval.getContigIndex() == curr_contig ) {
             if ( interval.getStart() < curr_position )
-                throw new GATKException("Out of order query: query position "+interval +" is located before "+
+                throw new ReviewedStingException("Out of order query: query position "+interval +" is located before "+
                         "the iterator's current position "+curr_contig + ":" + curr_position);
             if ( interval.getStop() < curr_query_end )
-                throw new GATKException("Unsupported querying sequence: current query interval " +
+                throw new ReviewedStingException("Unsupported querying sequence: current query interval " +
                         interval+" ends before the end of previous query interval ("+curr_query_end+")");
         }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java b/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
index 6e9eb88de..af895b262 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/features/refseq/RefSeqFeature.java
@@ -4,7 +4,7 @@ import org.broad.tribble.Feature;
 import org.broadinstitute.sting.gatk.refdata.Transcript;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 
@@ -60,7 +60,7 @@ public class RefSeqFeature implements Transcript, Feature {
 
     /** Genomic location of the n-th exon; throws an exception if n is out of bounds */
     public GenomeLoc getExonLocation(int n) {
-        if ( n >= exons.size() || n < 0 ) throw new GATKException("Index out-of-bounds. Transcript has " + exons.size() +" exons; requested: "+n);
+        if ( n >= exons.size() || n < 0 ) throw new ReviewedStingException("Index out-of-bounds. Transcript has " + exons.size() +" exons; requested: "+n);
         return exons.get(n);
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java
index 484d90fdf..29aefacc6 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackCreationException.java
@@ -23,7 +23,7 @@
 
 package org.broadinstitute.sting.gatk.refdata.tracks;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 
 /**
@@ -34,7 +34,7 @@ import org.broadinstitute.sting.utils.exceptions.GATKException;
  *
  * if we fail for some reason to make a track, throw this exception
  */
-public class RMDTrackCreationException extends GATKException {
+public class RMDTrackCreationException extends ReviewedStingException {
     public RMDTrackCreationException(String msg) {
         super(msg);
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/TribbleTrack.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/TribbleTrack.java
index 9694bcb24..4890bb9a0 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/TribbleTrack.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/TribbleTrack.java
@@ -30,7 +30,7 @@ import org.broad.tribble.FeatureSource;
 import org.broad.tribble.source.BasicFeatureSource;
 import org.broadinstitute.sting.gatk.refdata.utils.FeatureToGATKFeatureIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
@@ -115,7 +115,7 @@ public class TribbleTrack extends RMDTrack implements QueryableTrack {
         try {
             reader.close();
         } catch (IOException e) {
-            throw new GATKException("Unable to close reader " + reader.toString(),e);
+            throw new ReviewedStingException("Unable to close reader " + reader.toString(),e);
         }
         reader = null;
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
index 56cd44aa0..e0fc5dd52 100644
--- a/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
+++ b/java/src/org/broadinstitute/sting/gatk/refdata/tracks/builders/TribbleRMDTrackBuilder.java
@@ -36,7 +36,7 @@ import org.broad.tribble.util.LittleEndianOutputStream;
 import org.broadinstitute.sting.gatk.refdata.tracks.TribbleTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.classloader.PluginManager;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -227,7 +227,7 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
             locked = lock.sharedLock();
         }
         catch(FileSystemInabilityToLockException ex) {
-            throw new GATKException("Unexpected inability to lock exception", ex);
+            throw new ReviewedStingException("Unexpected inability to lock exception", ex);
         }
         Index idx;
         try {
@@ -294,7 +294,7 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
             return index;
         }
         catch(FileSystemInabilityToLockException ex) {
-            throw new GATKException("Unexpected inability to lock exception", ex);
+            throw new ReviewedStingException("Unexpected inability to lock exception", ex);
         }
         finally {
             if (locked) lock.unlock();
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java
index 2995723e1..888eb7e6e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/analyzeannotations/AnnotationDatum.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.analyzeannotations;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.Comparator;
 
@@ -114,7 +114,7 @@ public class AnnotationDatum implements Comparator<AnnotationDatum> {
     final public float calcTiTv( final int INDEX ) {
 
         if( ti[INDEX] < 0 || tv[INDEX] < 0 ) {
-            throw new GATKException( "Integer overflow detected! There are too many variants piled up in one annotation bin." );
+            throw new ReviewedStingException( "Integer overflow detected! There are too many variants piled up in one annotation bin." );
         }
 
         if( tv[INDEX] == 0 ) { // Don't divide by zero
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
index bd5406137..bfa1c4db5 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/HaplotypeScore.java
@@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.genotype.Haplotype;
 import org.broadinstitute.sting.utils.pileup.*;
 
@@ -197,7 +197,7 @@ public class HaplotypeScore implements InfoFieldAnnotation, StandardAnnotation {
         String b = haplotypeB.toString();
 
         if (a.length() != b.length())
-            throw new GATKException("Haplotypes a and b must be of same length");
+            throw new ReviewedStingException("Haplotypes a and b must be of same length");
 
         char chA, chB;
         char wc = REGEXP_WILDCARD.charAt(0);
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
index 3e49fac4a..1b7527416 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/VariantAnnotatorEngine.java
@@ -49,7 +49,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.helpers.DbSNPHelper;
 import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
 import org.broadinstitute.sting.gatk.walkers.annotator.genomicannotator.*;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.classloader.PackageUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
@@ -168,7 +168,7 @@ public class VariantAnnotatorEngine {
         Collection<VariantContext> results = this.annotateContext(tracker, ref, EMPTY_STRATIFIED_ALIGNMENT_CONTEXT, vc);
 
         if ( results.size() != 1 )
-            throw new GATKException("BUG: annotateContext call requires 1 resulting annotated VC, but got " + results);
+            throw new ReviewedStingException("BUG: annotateContext call requires 1 resulting annotated VC, but got " + results);
 
         return results.iterator().next();
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java
index fa67bf888..1b2c85b3e 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTable.java
@@ -33,7 +33,7 @@ import java.util.ArrayList;
 import java.util.HashMap;
 import java.util.List;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 /**
@@ -83,7 +83,7 @@ public class JoinTable
      */
     public void parseFromFile(String filename, String localBindingName, String localColumnName, String externalBindingName, String externalColumnName)  {
         if(parsedFromFile) {
-            throw new GATKException("parseFromFile(" + filename +", ..) called more than once");
+            throw new ReviewedStingException("parseFromFile(" + filename +", ..) called more than once");
         }
         parsedFromFile = true;
 
@@ -135,7 +135,7 @@ public class JoinTable
                     br.close();
                 }
             } catch(IOException e) {
-                throw new GATKException("Unable to close file: " + filename, e);
+                throw new ReviewedStingException("Unable to close file: " + filename, e);
             }
         }
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java
index c93c988a7..d3fcfd42a 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/JoinTableParser.java
@@ -31,7 +31,7 @@ import java.util.ArrayList;
 import java.util.Collections;
 import java.util.List;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
@@ -63,7 +63,7 @@ public class JoinTableParser
     public List<String> readHeader(BufferedReader br) throws IOException
     {
         if(header != null) {
-            throw new GATKException("readHeader(..) called more than once. Header is currently set to: " + header);
+            throw new ReviewedStingException("readHeader(..) called more than once. Header is currently set to: " + header);
         }
 
         header = Collections.unmodifiableList(parseHeader(br));
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
index caf5f93ec..b0588b9e4 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/annotator/genomicannotator/TranscriptToGenomicInfo.java
@@ -44,7 +44,7 @@ import org.broadinstitute.sting.gatk.walkers.Requires;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
 import org.broadinstitute.sting.gatk.walkers.Window;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 /**
@@ -973,7 +973,7 @@ public class TranscriptToGenomicInfo extends RodWalker<Integer, Integer> {
          */
         public int computeInitialCodingCoord() {
             if(!isProteinCodingTranscript()) {
-                throw new GATKException("This method should only be called for protein-coding transcripts");
+                throw new ReviewedStingException("This method should only be called for protein-coding transcripts");
             }
 
             if(positiveStrand)
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
index 7eec418f9..a58d71129 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/CoverageUtils.java
@@ -4,7 +4,7 @@ import net.sf.samtools.SAMReadGroupRecord;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 
@@ -57,7 +57,7 @@ public class CoverageUtils {
         } else if ( type == DoCOutputType.Partition.sample_by_platform_by_center ) {
             return String.format("%s_pl_%s_cn_%s",r.getSample(),r.getPlatform(),r.getSequencingCenter());
         } else {
-            throw new GATKException("Invalid type ID sent to getTypeID. This is a BUG!");
+            throw new ReviewedStingException("Invalid type ID sent to getTypeID. This is a BUG!");
         }
     }
 
@@ -119,7 +119,7 @@ public class CoverageUtils {
             try {
                 counts[BaseUtils.simpleBaseToBaseIndex(e.getBase())]++;
             } catch (ArrayIndexOutOfBoundsException exc) {
-                throw new GATKException("Expected a simple base, but actually received"+(char)e.getBase());
+                throw new ReviewedStingException("Expected a simple base, but actually received"+(char)e.getBase());
             }
         }
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
index 27a95f514..e93b579a6 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/coverage/DepthOfCoverageWalker.java
@@ -40,7 +40,7 @@ import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.io.File;
@@ -226,7 +226,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
                 partition.add(String.format("%s_pl_%s_cn_%s",rg.getSample(),rg.getPlatform(),rg.getSequencingCenter()));
             }
         } else {
-            throw new GATKException("Invalid aggregation type sent to getSamplesFromToolKit");
+            throw new ReviewedStingException("Invalid aggregation type sent to getSamplesFromToolKit");
         }
 
         return partition;
@@ -289,7 +289,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
                         getCorrectStream(partition, DoCOutputType.Aggregation.interval, DoCOutputType.FileType.statistics),
                         partition);
             } else {
-                throw new GATKException("Partition type "+partition.toString()+" had no entries. Please check that your .bam header has all appropriate partition types.");
+                throw new ReviewedStingException("Partition type "+partition.toString()+" had no entries. Please check that your .bam header has all appropriate partition types.");
             }
         }
 
@@ -766,7 +766,7 @@ public class DepthOfCoverageWalker extends LocusWalker<Map<DoCOutputType.Partiti
             int index = 0;
             for ( String s : namesInAg ) {
                 if ( ! s.equalsIgnoreCase(order.get(index)) ) {
-                    throw new GATKException("IDs are out of order for type "+t+"! Aggregator has different ordering");
+                    throw new ReviewedStingException("IDs are out of order for type "+t+"! Aggregator has different ordering");
                 }
                 index++;
             }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
index 3f3a205f9..ed2c06df1 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/fasta/FastaSequence.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.walkers.fasta;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.PrintStream;
 
@@ -23,7 +23,7 @@ public class FastaSequence {
     }
 
     public void setName(String name) {
-        if ( printedHeader ) throw new GATKException("Can not set name for FASTA record: header is already printed.");
+        if ( printedHeader ) throw new ReviewedStingException("Can not set name for FASTA record: header is already printed.");
         this.name = name;
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java b/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
index c29711b66..225cdecc3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/filters/FiltrationContextWindow.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.filters;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.*;
 
@@ -80,9 +80,9 @@ public class FiltrationContextWindow {
      */
     public FiltrationContext[] getWindow(int elementsToLeft, int elementsToRight) {
         if ( elementsToLeft > maxWindowElements() || elementsToRight > maxWindowElements() )
-            throw new GATKException("Too large a window requested");
+            throw new ReviewedStingException("Too large a window requested");
         if ( elementsToLeft < 0 || elementsToRight < 0 )
-            throw new GATKException("Window size cannot be negative");
+            throw new ReviewedStingException("Window size cannot be negative");
 
         FiltrationContext[] array = new FiltrationContext[elementsToLeft + elementsToRight + 1];
         ListIterator<FiltrationContext> iter = window.listIterator(currentContext - elementsToLeft);
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
index 547ddde15..46a935f78 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
@@ -30,7 +30,7 @@ import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
@@ -192,7 +192,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
 
         public void incrementFrequency() {
             if ( frequency == 2 * N )
-                throw new GATKException("Frequency was incremented past N; how is this possible?");
+                throw new ReviewedStingException("Frequency was incremented past N; how is this possible?");
             frequency++;
 
             double greedy = VALUE_NOT_CALCULATED;
@@ -219,7 +219,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
                 // so we can ignore that case
             }
             if ( greedyIndex == -1 )
-                throw new GATKException("There is no best choice for a new alternate allele; how is this possible?");
+                throw new ReviewedStingException("There is no best choice for a new alternate allele; how is this possible?");
 
             if ( indexes[greedyIndex] == GenotypeType.HET.ordinal() )
                 indexes[greedyIndex] = GenotypeType.HOM.ordinal();
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
index e3afe847b..25ba13061 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/SimpleIndelCalculationModel.java
@@ -5,7 +5,7 @@ import org.broad.tribble.util.variantcontext.Genotype;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.*;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.*;
@@ -72,7 +72,7 @@ public class SimpleIndelCalculationModel extends GenotypeCalculationModel {
                 alleles.add( Allele.create(bestEvent.substring(1), true ));
                 loc = GenomeLocParser.setStop(loc, loc.getStop() + bestEvent.length()-1);
             } else
-                throw new GATKException("Internal error (probably a bug): event does not conform to expected format: "+ bestEvent);
+                throw new ReviewedStingException("Internal error (probably a bug): event does not conform to expected format: "+ bestEvent);
         }
 
         VariantContext vc = new VariantContext("UG_Indel_call", loc.getContig(), loc.getStart(), loc.getStop(), alleles, new HashMap<String, Genotype>() /* genotypes */,
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 74f025908..d785bf595 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -31,7 +31,7 @@ import net.sf.samtools.util.SequenceUtil;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.commandline.*;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.interval.IntervalUtils;
@@ -334,7 +334,7 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
             do {
                 currentInterval = intervals.hasNext() ? intervals.next() : null;
             } while ( currentInterval != null && (readLoc == null || currentInterval.isBefore(readLoc)) );
-        } catch (GATKException e) {
+        } catch (ReviewedStingException e) {
             throw new UserException.MissortedFile(new File(intervalsFile), " *** Are you sure that your interval file is sorted? If not, you must use the --targetIntervalsAreNotSorted argument. ***", e);
         }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
index e0b627d3d..7451565c8 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/CycleQualityWalker.java
@@ -30,7 +30,7 @@ import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.collections.PrimitivePair;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
@@ -81,7 +81,7 @@ public class CycleQualityWalker extends ReadWalker<Integer,Integer> {
     private Map<String,CycleStats[]> cyclesByLibraryMapOrig = null;
 
     public void initialize() {
-        if ( PREFIX == null ) throw new GATKException("Prefix for output file(s) must be specified");
+        if ( PREFIX == null ) throw new ReviewedStingException("Prefix for output file(s) must be specified");
         cyclesByLaneMap = new HashMap<String,CycleStats[]>();
         cyclesByLibraryMap = new HashMap<String,CycleStats[]>();
         cyclesByLaneMapOrig = new HashMap<String,CycleStats[]>();
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
index ec3a9b677..6ad0340a4 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ReadValidationWalker.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.gatk.walkers.qc;
 import org.broadinstitute.sting.gatk.refdata.ReadMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.ReadWalker;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import net.sf.samtools.SAMRecord;
 import net.sf.samtools.SAMFileWriter;
 
@@ -58,7 +58,7 @@ public class ReadValidationWalker extends ReadWalker<SAMRecord, SAMRecord> {
         try {
             m = MessageDigest.getInstance("MD5");
         } catch (NoSuchAlgorithmException e) {
-            throw new GATKException("Unable to get the MD5 algorithm. Get a more eXtreme version of JAVA!@!@!!");
+            throw new ReviewedStingException("Unable to get the MD5 algorithm. Get a more eXtreme version of JAVA!@!@!!");
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
index d06b2035d..72ba37830 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/qc/ValidatingPileupWalker.java
@@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 
@@ -140,7 +140,7 @@ public class ValidatingPileupWalker extends LocusWalker<Integer, ValidationStats
         else if( pileup.hasIndelGenotype() )
             return pileup.getIndelGenotype();
         else
-            throw new GATKException("Unsupported pileup type: " + pileup);
+            throw new ReviewedStingException("Unsupported pileup type: " + pileup);
     }
 }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
index 2f46350a1..2be2da8b0 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/recalibration/RecalDataManager.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.gatk.walkers.recalibration;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
@@ -326,7 +326,7 @@ public class RecalDataManager {
             if( attr instanceof String ) {
                 colorSpace = ((String)attr).getBytes();
             } else {
-                throw new GATKException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));
+                throw new ReviewedStingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));
             }
 
             // Loop over the read and calculate first the inferred bases from the color and then check if it is consistent with the read
@@ -373,7 +373,7 @@ public class RecalDataManager {
                 if( attr instanceof String ) {
                     colorSpace = ((String)attr).substring(1).getBytes(); // trim off the Sentinel
                 } else {
-                    throw new GATKException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));
+                    throw new ReviewedStingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_ATTRIBUTE_TAG, read.getReadName()));
                 }
 
                 for( byte color : colorSpace ) {
@@ -448,7 +448,7 @@ public class RecalDataManager {
                 colorSpaceQuals = x.getBytes();
                 SAMUtils.fastqToPhred(colorSpaceQuals);
             } else {
-                throw new GATKException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_QUAL_ATTRIBUTE_TAG, read.getReadName()));
+                throw new ReviewedStingException(String.format("Value encoded by %s in %s isn't a string!", RecalDataManager.COLOR_SPACE_QUAL_ATTRIBUTE_TAG, read.getReadName()));
             }
 
             for( int iii = 1; iii < inconsistency.length - 1; iii++ ) {
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java
index a76c034ad..86e99e514 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/CountVariants.java
@@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 
 @Analysis(name = "Count Variants", description = "Counts different classes of variants in the sample")
@@ -112,7 +112,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                 nComplex++;
                 break;
             default:
-                throw new GATKException("Unexpected VariantContext type " + vc1.getType());
+                throw new ReviewedStingException("Unexpected VariantContext type " + vc1.getType());
         }
 
         for (Genotype g : vc1.getGenotypes().values()) {
@@ -130,7 +130,7 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
                     nHomVar++;
                     break;
                 default:
-                    throw new GATKException("BUG: Unexpected genotype type: " + g);
+                    throw new ReviewedStingException("BUG: Unexpected genotype type: " + g);
             }
         }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
index 0a975aad0..208504588 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/GenotypeConcordance.java
@@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.utils.TableType;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
@@ -141,7 +141,7 @@ public class GenotypeConcordance extends VariantEvaluator implements StandardEva
             } else if ( x == 1 ) {
                 return String.valueOf(falsePositiveHist[y]);
             } else {
-                throw new GATKException( "Unknown row in " + getName() + ", row = " + x );
+                throw new ReviewedStingException( "Unknown row in " + getName() + ", row = " + x );
             }
         }
 
@@ -553,7 +553,7 @@ class SampleSummaryStats implements TableType {
 
             final long[][] stats = sampleStats.concordanceStats.get(sample);
             final double[] summary = concordanceSummary.get(sample);
-            if( stats == null ) { throw new GATKException( "SampleStats and SampleSummaryStats contain different samples! sample = " + sample ); }
+            if( stats == null ) { throw new ReviewedStingException( "SampleStats and SampleSummaryStats contain different samples! sample = " + sample ); }
 
             long numer, denom;
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java
index 36edbb5dc..007a2c70a 100644
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/IndelLengthHistogram.java
@@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.utils.TableType;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 /**
  * IF THERE IS NO JAVADOC RIGHT HERE, YELL AT chartl
@@ -77,7 +77,7 @@ public class IndelLengthHistogram extends VariantEvaluator {
 
         private int len2index(int len) {
             if ( len > limit || len < -limit ) {
-                throw new GATKException("Indel length exceeds limit of "+limit+" please increase indel limit size");
+                throw new ReviewedStingException("Indel length exceeds limit of "+limit+" please increase indel limit size");
             }
             return len + limit;
         }
@@ -105,7 +105,7 @@ public class IndelLengthHistogram extends VariantEvaluator {
             } else if ( vc1.isDeletion() ) {
                 indelHistogram.update(-vc1.getReference().length());
             } else {
-                throw new GATKException("Indel type that is not insertion or deletion.");
+                throw new ReviewedStingException("Indel type that is not insertion or deletion.");
             }
         }
 
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java
index c9b198bf1..e400297f3 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/MendelianViolationEvaluator.java
@@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.List;
 import java.util.Arrays;
@@ -138,7 +138,7 @@ public class MendelianViolationEvaluator extends VariantEvaluator {
                         label = "KidHomVar_ParentHomRef";
                         KidHomVar_ParentHomRef++;
                     } else {
-                        throw new GATKException("BUG: unexpected child genotype class " + childG);
+                        throw new ReviewedStingException("BUG: unexpected child genotype class " + childG);
                     }
 
                     return "MendelViolation=" + label;
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java
index e3e88ab92..961121849 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/SimpleMetricsByAC.java
@@ -8,7 +8,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.utils.TableType;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
 
@@ -74,7 +74,7 @@ public class SimpleMetricsByAC extends VariantEvaluator implements StandardEval
                 case 3: return String.valueOf(nTi + nTv);
                 case 4: return String.valueOf(ratio(nTi, nTv));
                 default:
-                    throw new GATKException("Unexpected column " + i);
+                    throw new ReviewedStingException("Unexpected column " + i);
             }
         }
     }
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
index 76b73035a..11c9bf0b7 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/VariantEvalWalker.java
@@ -45,7 +45,7 @@ import org.broadinstitute.sting.playground.utils.report.ReportMarshaller;
 import org.broadinstitute.sting.playground.utils.report.VE2ReportFactory;
 import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat;
 import org.broadinstitute.sting.playground.utils.report.utils.Node;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.classloader.PackageUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.commandline.Argument;
@@ -558,7 +558,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
                             if ( interesting != null ) interestingReasons.add(interesting);
                             break;
                         default:
-                            throw new GATKException("BUG: Unexpected evaluation order " + evaluation);
+                            throw new ReviewedStingException("BUG: Unexpected evaluation order " + evaluation);
                     }
                 }
             }
@@ -708,7 +708,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
         for ( EvaluationContext group : contexts ) {
             String[] parts = group.getDisplayName().split(CONTEXT_SEPARATOR);
             if ( parts.length != N_CONTEXT_NAME_PARTS ) {
-                throw new GATKException("Unexpected number of eval name parts " + group.getDisplayName() + " length = " + parts.length + ", expected " + N_CONTEXT_NAME_PARTS);
+                throw new ReviewedStingException("Unexpected number of eval name parts " + group.getDisplayName() + " length = " + parts.length + ", expected " + N_CONTEXT_NAME_PARTS);
             } else {
                 for ( int i = 0; i < parts.length; i++ )
                     nameSizes[i] = Math.max(nameSizes[i], parts[i].length());
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
index a7cce23ad..1a7152b49 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantGaussianMixtureModel.java
@@ -28,7 +28,7 @@ package org.broadinstitute.sting.gatk.walkers.variantrecalibration;
 import org.apache.log4j.Logger;
 import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
 import org.broadinstitute.sting.utils.exceptions.UserException;
@@ -699,7 +699,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
 
                     logger.warn("About to throw exception due to numerical instability. Try running with fewer annotations and then with fewer Gaussians. " +
                             "It is best to only use the annotations which appear to be Gaussianly distributed for this Gaussian mixture model.");
-                    throw new GATKException("Numerical Instability! Found NaN after performing log10: " + pVarInClusterLog10[kkk] + ", cluster = " + kkk + ", variant index = " + iii);
+                    throw new ReviewedStingException("Numerical Instability! Found NaN after performing log10: " + pVarInClusterLog10[kkk] + ", cluster = " + kkk + ", variant index = " + iii);
                 }
             }
 
@@ -709,7 +709,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
                 if( Double.isNaN(pVarInCluster[kkk][iii]) ) {
                     logger.warn("About to throw exception due to numerical instability. Try running with fewer annotations and then with fewer Gaussians. " +
                             "It is best to only use the annotations which appear to be Gaussianly distributed for this Gaussian mixture model.");
-                    throw new GATKException("Numerical Instability! Found NaN after rescaling log10 values: " + pVarInCluster[kkk][iii] + ", cluster = " + kkk + ", variant index = " + iii);
+                    throw new ReviewedStingException("Numerical Instability! Found NaN after rescaling log10 values: " + pVarInCluster[kkk][iii] + ", cluster = " + kkk + ", variant index = " + iii);
                 }
             }
         }
@@ -775,7 +775,7 @@ public final class VariantGaussianMixtureModel extends VariantOptimizationModel
                 if( Double.isNaN(prob) ) {
                     logger.warn("About to throw exception due to numerical instability. Try running with fewer annotations and then with fewer Gaussians. " +
                             "It is best to only use the annotations which appear to be Gaussianly distributed for this Gaussian mixture model.");
-                    throw new GATKException("Numerical Instability! Found NaN in M-step: " + pVarInCluster[kkk][iii] + ", cluster = " + kkk + ", variant index = " + iii);
+                    throw new ReviewedStingException("Numerical Instability! Found NaN in M-step: " + pVarInCluster[kkk][iii] + ", cluster = " + kkk + ", variant index = " + iii);
                 }
                 sumProb += prob;
                 for( int jjj = 0; jjj < numAnnotations; jjj++ ) {
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
index 762b64e87..a263008fc 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/BeagleOutputByDepthWalker.java
@@ -35,7 +35,7 @@ import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.io.PrintStream;
@@ -156,7 +156,7 @@ public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
                 else if (compGenotype.isHomVar())
                     hg = 2;
                 else
-                    throw new GATKException("Bug! invalid genotype!");
+                    throw new ReviewedStingException("Bug! invalid genotype!");
 
                 if (postbglGenotype.isNoCall())
                     bg = -1;
@@ -167,7 +167,7 @@ public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
                 else if (postbglGenotype.isHomVar())
                     bg = 2;
                 else
-                    throw new GATKException("Bug! invalid genotype!");
+                    throw new ReviewedStingException("Bug! invalid genotype!");
 
 
                 if (prebglGenotype.isNoCall())
@@ -179,7 +179,7 @@ public class BeagleOutputByDepthWalker extends RodWalker<Integer, Integer> {
                 else if (prebglGenotype.isHomVar())
                     pg = 2;
                 else
-                    throw new GATKException("Bug! invalid genotype!");
+                    throw new ReviewedStingException("Bug! invalid genotype!");
 
                 outputWriter.format("%d %d %d %d\n",dp, hg, pg, bg);
 
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java
index ce24c5fc5..2c907ebd1 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DesignFileGeneratorWalker.java
@@ -7,7 +7,7 @@ import org.broadinstitute.sting.gatk.refdata.*;
 import org.broadinstitute.sting.gatk.refdata.features.refseq.RefSeqFeature;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.commandline.Output;
@@ -196,7 +196,7 @@ class IntervalInfoBuilder {
                     }
                 }
             } else {
-                throw new GATKException("Attempting to update an IntervalInfoBuilder twice with the same (non-TCGA) gene: "+gene);
+                throw new ReviewedStingException("Attempting to update an IntervalInfoBuilder twice with the same (non-TCGA) gene: "+gene);
             }
         } else {
 
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java
index bf5d96984..f50e33550 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/DownsamplingValidationWalker.java
@@ -29,7 +29,7 @@ import org.broadinstitute.sting.gatk.refdata.features.samread.SAMReadFeature;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.commandline.Argument;
 
@@ -71,7 +71,7 @@ public class DownsamplingValidationWalker extends LocusWalker<Integer,Long> {
         int matchingReadsFound = 0;
         if(unsampledReadsStartingAtThisLocus.isEmpty()) {
             if(!sampledReadsStartingAtThisLocus.isEmpty())
-                throw new GATKException("Downsampler hallucinated a read starting at locus "+ref.getLocus());
+                throw new ReviewedStingException("Downsampler hallucinated a read starting at locus "+ref.getLocus());
         }
         else {
             boolean foundMatch = false;
@@ -86,10 +86,10 @@ public class DownsamplingValidationWalker extends LocusWalker<Integer,Long> {
             }
 
             if(!foundMatch)
-                throw new GATKException("Downsampler failed to include any read starting at locus "+ref.getLocus());
+                throw new ReviewedStingException("Downsampler failed to include any read starting at locus "+ref.getLocus());
 
             if(matchingReadsFound > maxExpectedNumberOfReads)
-                throw new GATKException("Downsampler found too many reads starting at locus "+ref.getLocus());
+                throw new ReviewedStingException("Downsampler found too many reads starting at locus "+ref.getLocus());
         }
 
         return matchingReadsFound;
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
index 797a146c2..5401fa360 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/MendelianViolationClassifier.java
@@ -21,7 +21,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
 import org.broadinstitute.sting.gatk.walkers.varianteval.MendelianViolationEvaluator;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 
@@ -420,7 +420,7 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
                 } else if ( isOppositeHomozygote(varContext) ) {
                     violation = assessOppositeHomozygote(varContext,tracker,reference,context);
                 } else {
-                    throw new GATKException("Mendelian violation that is neither deNovo nor opposite homozygote. Should never see this.");
+                    throw new ReviewedStingException("Mendelian violation that is neither deNovo nor opposite homozygote. Should never see this.");
                 }
             } else {
                 violation = new MendelianViolation(varContext,MendelianViolationType.NONE);
@@ -464,7 +464,7 @@ public class MendelianViolationClassifier extends LocusWalker<MendelianViolation
         if ( ! trio.isFiltered() ) {
             Allele parental = trio.getGenotype(trioStructure.mom).getAllele(0); // guaranteed homozygous
             if ( parental.getBases().length < 1 ) {
-                throw new GATKException("Parental bases have length zero at "+trio.toString());
+                throw new ReviewedStingException("Parental bases have length zero at "+trio.toString());
             }
 
             Map<String,StratifiedAlignmentContext> splitContext = StratifiedAlignmentContext.splitContextBySample(context.getBasePileup());
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java
index 2ead0e1e0..7d0439eaf 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/QualityScoreByStrandWalker.java
@@ -28,7 +28,7 @@ package org.broadinstitute.sting.oneoffprojects.walkers;
 import java.io.File;
 import java.io.IOException;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -210,7 +210,7 @@ class StrandedCounts {
 
     public void updateReadPair( int fQual, int rQual, int fOff, int rOff ) {  // hehe f Off
         if ( rOff < 0 || fOff < 0 )
-	    throw new GATKException("Offset is negative. Should never happen.");
+	    throw new ReviewedStingException("Offset is negative. Should never happen.");
 	forwardCountsByOffset[fOff][fQual < 0 ? 0 : fQual > 40 ? 40 : fQual]++;
         reverseCountsByOffset[rOff][rQual < 0 ? 0 : rQual > 40 ? 40 : rQual]++;
     }
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java
index 6c7ab7d59..2a10f1ad5 100644
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/TestReadFishingWalker.java
@@ -34,7 +34,7 @@ import org.broadinstitute.sting.alignment.bwa.c.BWACAligner;
 import org.broadinstitute.sting.alignment.Alignment;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import net.sf.samtools.SAMRecord;
@@ -128,7 +128,7 @@ public class TestReadFishingWalker extends ReadWalker<Integer,Long> {
                 System.arraycopy(referenceSequence.getBases(),eventStart,revisedReference,eventStart+eventLength,bufferWidth);
             }
             else
-                throw new GATKException("Invalid indel type: " + type);
+                throw new ReviewedStingException("Invalid indel type: " + type);
 
             aligners.put(GenomeLocParser.createGenomeLoc(contig,start,stop),new BWACAligner(revisedReference,new BWAConfiguration()));
             if(++numAlignersCreated % 100 == 0)
diff --git a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
index 34ab9fc64..d17bffcfc 100755
--- a/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
+++ b/java/src/org/broadinstitute/sting/oneoffprojects/walkers/VCF4WriterTestWalker.java
@@ -11,7 +11,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrde
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
 import org.broadinstitute.sting.gatk.walkers.RodWalker;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 
@@ -95,7 +95,7 @@ public class VCF4WriterTestWalker extends RodWalker<Integer, Integer> {
                     out.printf("Read %d header lines%n", header.getMetaData().size());
                 }
                 catch (FileNotFoundException e ) {
-                    throw new GATKException(e.getMessage());
+                    throw new ReviewedStingException(e.getMessage());
                 }
 
                 final Set<String> vcfSamples = header.getGenotypeSamples();
diff --git a/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java b/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java
index e1c977501..ddac5f58f 100644
--- a/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java
+++ b/java/src/org/broadinstitute/sting/playground/analyzeconcordance/AnalyzeConcordance.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.playground.analyzeconcordance;
 
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 import org.broadinstitute.sting.commandline.Argument;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.utils.PathUtils;
@@ -92,7 +92,7 @@ public class AnalyzeConcordance extends CommandLineProgram {
 			generateHtmlReport();
 			logger.info("...Done!");
         } catch (Exception e) {
-            throw new GATKException("Error analyzing concordance", e);
+            throw new ReviewedStingException("Error analyzing concordance", e);
         }
 
         return result;
@@ -102,7 +102,7 @@ public class AnalyzeConcordance extends CommandLineProgram {
         // create the output directory where all the data tables and plots will go
         File outputDir = new File(this.outputDir);
         if (!outputDir.exists() && !outputDir.mkdirs()) {
-            throw new GATKException("Couldn't create directory: " + this.outputDir);
+            throw new ReviewedStingException("Couldn't create directory: " + this.outputDir);
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/playground/examples/SampleXmlMarshaller.java b/java/src/org/broadinstitute/sting/playground/examples/SampleXmlMarshaller.java
index 8468d87f5..c5f4c7efb 100755
--- a/java/src/org/broadinstitute/sting/playground/examples/SampleXmlMarshaller.java
+++ b/java/src/org/broadinstitute/sting/playground/examples/SampleXmlMarshaller.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.playground.examples;
 
 import org.apache.log4j.BasicConfigurator;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.simpleframework.xml.Element;
 import org.simpleframework.xml.Root;
 import org.simpleframework.xml.Serializer;
@@ -121,7 +121,7 @@ public class SampleXmlMarshaller {
             SampleXmlMarshaller example = serializer.read(SampleXmlMarshaller.class, source);
             return example;
         } catch (Exception e) {
-            throw new GATKException("Failed to marshal the data to file " + filename,e);
+            throw new ReviewedStingException("Failed to marshal the data to file " + filename,e);
         }
     }
 }
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
index 2aeff6db0..74329fd90 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/LocusMismatchWalker.java
@@ -39,7 +39,7 @@ import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection
 import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
 import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
@@ -155,7 +155,7 @@ public class LocusMismatchWalker extends LocusWalker<String,Integer> implements
         if ( g.isHomRef() ) return "HOM-REF";
         else if ( g.isHet() ) return "HET";
         else if ( g.isHom() ) return "HOM-NONREF";
-        else throw new GATKException("Unexpected genotype in getGenotypeClass " + g);
+        else throw new ReviewedStingException("Unexpected genotype in getGenotypeClass " + g);
     }
 
     public boolean useRead( PileupElement e ) {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java
index 433f0aecf..c331596f7 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/ReadBackedPhasingWalker.java
@@ -38,7 +38,7 @@ import org.broadinstitute.sting.gatk.walkers.*;
 import org.broadinstitute.sting.commandline.Argument;
 import org.broadinstitute.sting.commandline.Output;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.vcf.VCFUtils;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
@@ -301,7 +301,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
                         }
                     }
                     if (logger.isDebugEnabled() && (phasingSiteIndex == -1 || phasingSiteIndex == 0))
-                        throw new GATKException("Internal error: could NOT find vr and/or prevVr!");
+                        throw new ReviewedStingException("Internal error: could NOT find vr and/or prevVr!");
 
                     if (sampleWindowVaList.size() > maxPhaseSites) {
                         logger.warn("Trying to phase sample " + samp + " at locus " + VariantContextUtils.getLocation(vc) + " within a window of " + cacheWindow + " bases yields " + sampleWindowVaList.size() + " heterozygous sites to phase:\n" + toStringVRL(sampleWindowVaList));
@@ -433,7 +433,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
 
     public static void ensurePhasing(BialleleSNP curBiall, BialleleSNP prevBiall, Haplotype hap) {
         if (hap.size() < 2)
-            throw new GATKException("LOGICAL ERROR: Only considering haplotypes of length > 2!");
+            throw new ReviewedStingException("LOGICAL ERROR: Only considering haplotypes of length > 2!");
 
         byte prevBase = hap.getBase(0); // The 1st base in the haplotype
         byte curBase = hap.getBase(1);  // The 2nd base in the haplotype
@@ -746,7 +746,7 @@ public class ReadBackedPhasingWalker extends RodWalker<PhasingStatsAndOutput, Ph
         private Haplotype complement(Haplotype hap) {
             int numSites = bialleleSNPs.length;
             if (hap.size() != numSites)
-                throw new GATKException("INTERNAL ERROR: hap.size() != numSites");
+                throw new ReviewedStingException("INTERNAL ERROR: hap.size() != numSites");
 
             // Take the other base at EACH position of the Haplotype:
             byte[] complementBases = new byte[numSites];
@@ -954,7 +954,7 @@ class Haplotype extends BaseArray implements Cloneable {
 
     public void updateBase(int index, Byte base) {
         if (base == null) {
-            throw new GATKException("Internal error: CANNOT have null for a missing Haplotype base!");
+            throw new ReviewedStingException("Internal error: CANNOT have null for a missing Haplotype base!");
         }
         super.updateBase(index, base);
     }
@@ -1054,7 +1054,7 @@ class Read extends BaseArray {
 
         int sz = this.bases.length;
         if (sz != hap.bases.length)
-            throw new GATKException("Read and Haplotype should have same length to be compared!");
+            throw new ReviewedStingException("Read and Haplotype should have same length to be compared!");
 
         for (int i = 0; i < sz; i++) {
             Byte thisBase = this.getBase(i);
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java
index eefbd87d4..614e266d6 100755
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/hybridselection/CoverageAcrossBaitsWalker.java
@@ -33,7 +33,7 @@ import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.walkers.By;
 import org.broadinstitute.sting.gatk.walkers.DataSource;
 import org.broadinstitute.sting.gatk.walkers.LocusWalker;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.commandline.Argument;
@@ -90,7 +90,7 @@ public class CoverageAcrossBaitsWalker extends LocusWalker<Pair<Integer, Integer
         IntervalRod intervalROD = tracker.lookup("interval",IntervalRod.class);
 
         GenomeLoc interval = intervalROD == null ? null : intervalROD.getLocation();
-        if (interval == null) { throw new GATKException("No intervals at locus; should not happen"); }
+        if (interval == null) { throw new ReviewedStingException("No intervals at locus; should not happen"); }
         int offset = (int)(context.getPosition() - interval.getStart());
 
         int depth[] = new int[2];
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java
index 7cd398031..de9e549ee 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/Biallele.java
@@ -25,7 +25,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.phasing;
 
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -36,7 +36,7 @@ public class Biallele {
 
     public Biallele(Genotype gt) {
         if (gt.getPloidy() != 2)
-            throw new GATKException("Biallele must have ploidy of 2!");
+            throw new ReviewedStingException("Biallele must have ploidy of 2!");
 
         this.top = gt.getAllele(0);
         this.bottom = gt.getAllele(1);
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java
index e5b86287a..948f6a40f 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/phasing/BialleleSNP.java
@@ -26,7 +26,7 @@ package org.broadinstitute.sting.playground.gatk.walkers.phasing;
 import org.broad.tribble.util.variantcontext.Allele;
 import org.broad.tribble.util.variantcontext.Genotype;
 import org.broadinstitute.sting.utils.BaseUtils;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 public class BialleleSNP extends Biallele {
 
@@ -34,9 +34,9 @@ public class BialleleSNP extends Biallele {
         super(gt);
 
         if (getTopAllele().getBases().length != 1)
-            throw new GATKException("LOGICAL ERROR: BialleleSNP may not contain non-SNP site!");
+            throw new ReviewedStingException("LOGICAL ERROR: BialleleSNP may not contain non-SNP site!");
         if (getBottomAllele().getBases().length != 1)
-            throw new GATKException("LOGICAL ERROR: BialleleSNP may not contain non-SNP site!");
+            throw new ReviewedStingException("LOGICAL ERROR: BialleleSNP may not contain non-SNP site!");
     }
 
     public byte getTopBase() {
@@ -62,7 +62,7 @@ public class BialleleSNP extends Biallele {
         else if (BaseUtils.basesAreEqual(base, botBase))
             return topBase;
         else
-            throw new GATKException("LOGICAL ERROR: base MUST match either TOP or BOTTOM!");
+            throw new ReviewedStingException("LOGICAL ERROR: base MUST match either TOP or BOTTOM!");
     }
 
     public static byte getSingleBase(byte[] bases) {
diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java
index 98519ccc7..7e2e7b794 100644
--- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java
+++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/validation/RodSystemValidationWalker.java
@@ -10,7 +10,7 @@ import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrde
 import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
 import org.broadinstitute.sting.gatk.walkers.*;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
 import java.math.BigInteger;
@@ -49,7 +49,7 @@ public class RodSystemValidationWalker extends RodWalker<Integer,Integer> {
         try {
             digest = MessageDigest.getInstance("MD5");
         } catch (NoSuchAlgorithmException e) {
-            throw new GATKException("Unable to find MD5 checksumer");
+            throw new ReviewedStingException("Unable to find MD5 checksumer");
         }
         out.println("Header:");
         // enumerate the list of ROD's we've loaded
diff --git a/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java b/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java
index f85f13da2..c22105ed5 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/GenomicMap.java
@@ -49,7 +49,7 @@ import net.sf.samtools.SAMRecord;
 
 import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
 import org.broadinstitute.sting.utils.*;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.sam.AlignmentUtils;
 import org.broadinstitute.sting.utils.collections.Pair;
@@ -77,8 +77,8 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 	 * @param c mapping of the custom contig sequence onto intervals on the master reference
 	 */
 	public void addCustomContig(String name, Collection<GenomeLoc> c) {
-		if ( name == null ) throw new GATKException("Custom contig name can not be null");
-		if ( map.containsKey(name)) throw new GATKException("Custom contig "+name+" already exists");
+		if ( name == null ) throw new ReviewedStingException("Custom contig name can not be null");
+		if ( map.containsKey(name)) throw new ReviewedStingException("Custom contig "+name+" already exists");
 		map.put(name, c);
 	}
 	
@@ -184,7 +184,7 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 					p2 = p1;
 					while ( p2 < line.length() && line.charAt(p2) != ',') p2++; // next comma or end-of-line
 				}
-				if ( segments.size() == 0 ) throw new GATKException("Line "+line+" has no intervals specified");
+				if ( segments.size() == 0 ) throw new ReviewedStingException("Line "+line+" has no intervals specified");
 				addCustomContig(name, segments);
 			}
 			reader.close();
@@ -279,7 +279,7 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 			case S: // soft clip
 			case H: // or hard clip - these are not included in getAlignmentStart, so pass them through
 				if ( k != 0 && k != N-1 ) // paranoid
-					throw new GATKException("Don't know what to do with S or N cigar element that is not at the either end of the cigar. Cigar: "+
+					throw new ReviewedStingException("Don't know what to do with S or N cigar element that is not at the either end of the cigar. Cigar: "+
 							r.getCigarString());
 			case I: // insertions are passed through as well
 				newCigar.add(new CigarElement(len,ce.getOperator()));
@@ -377,7 +377,7 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 	 */
 	private Pair<PushbackIterator<GenomeLoc>,Integer> seekForward(Collection<GenomeLoc> segments,int position) {
 		
-		if ( position < 1 ) throw new GATKException("Position "+position + " is outside of custom contig boundaries");
+		if ( position < 1 ) throw new ReviewedStingException("Position "+position + " is outside of custom contig boundaries");
 		
 		PushbackIterator<GenomeLoc> iter = new PushbackIterator<GenomeLoc>(segments.iterator());
 		
@@ -392,7 +392,7 @@ public class GenomicMap implements Iterable<Map.Entry<String, Collection<GenomeL
 			position -= length;
 		}
 		// if we get here, position is to the right of the last segment; not good.
-		throw new GATKException("Position "+position + " is outside of custom contig boundaries");
+		throw new ReviewedStingException("Position "+position + " is outside of custom contig boundaries");
 	}
 
 	private long contigLength(Collection<GenomeLoc> segments) {
diff --git a/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java b/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java
index d86934baa..781a6fc9c 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/ProcessUtils.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.playground.utils;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.text.XReadLines;
 import org.apache.log4j.Logger;
 
@@ -60,7 +60,7 @@ public class ProcessUtils {
 
 			return result;
 		} catch (Exception e) {
-			throw new GATKException("Error running command:" + command, e);
+			throw new ReviewedStingException("Error running command:" + command, e);
 		}
 	}
 }
diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java b/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java
index 4308d93c3..46b23719d 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/report/AnalysisModuleScanner.java
@@ -26,7 +26,7 @@ package org.broadinstitute.sting.playground.utils.report;
 import org.broadinstitute.sting.playground.utils.report.tags.Analysis;
 import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
 import org.broadinstitute.sting.playground.utils.report.tags.Param;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.lang.annotation.Annotation;
 import java.lang.reflect.Field;
@@ -73,7 +73,7 @@ public class AnalysisModuleScanner {
     /** scan the class and find all appropriate fields and tables */
     public void scan() {
         if (cls == null || !cls.isAnnotationPresent(Analysis.class))
-            throw new GATKException("The class passed in cannot be null, " + "" +
+            throw new ReviewedStingException("The class passed in cannot be null, " + "" +
                                      "and must contain the @Analysis annotation, class " + cls + " was the input");
 
         // get the annotation off of the class
diff --git a/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java b/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java
index 34314a4f7..1dc360797 100644
--- a/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java
+++ b/java/src/org/broadinstitute/sting/playground/utils/report/ReportMarshaller.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.playground.utils.report;
 import org.broadinstitute.sting.playground.utils.report.templates.ReportFormat;
 import org.broadinstitute.sting.playground.utils.report.utils.ComplexDataUtils;
 import org.broadinstitute.sting.playground.utils.report.utils.Node;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.*;
 import java.lang.reflect.Field;
@@ -195,7 +195,7 @@ public class ReportMarshaller {
             else
                 node.addAllChildren(nodes);
         } catch (IllegalAccessException e) {
-            throw new GATKException("Unable to access field " + f);
+            throw new ReviewedStingException("Unable to access field " + f);
         }
     }
 }
diff --git a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
index d819c7502..92574d4ad 100644
--- a/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
+++ b/java/src/org/broadinstitute/sting/queue/extensions/gatk/GATKExtensionsGenerator.java
@@ -39,7 +39,7 @@ import org.broadinstitute.sting.gatk.io.stubs.SAMFileReaderArgumentTypeDescripto
 import org.broadinstitute.sting.gatk.io.stubs.SAMFileWriterArgumentTypeDescriptor;
 import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackManager;
 import org.broadinstitute.sting.gatk.walkers.Walker;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.IOException;
@@ -94,7 +94,7 @@ public class GATKExtensionsGenerator extends CommandLineProgram {
     protected int execute() {
         try {
             if (!outputDirectory.isDirectory() && !outputDirectory.mkdirs())
-                throw new GATKException("Unable to create output directory: " + outputDirectory);
+                throw new ReviewedStingException("Unable to create output directory: " + outputDirectory);
 
             for (Class<? extends CommandLineProgram> clp: clpManager.getValues()) {
 
diff --git a/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java b/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java
index 978920d81..50d5e8dda 100644
--- a/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java
+++ b/java/src/org/broadinstitute/sting/utils/CardinalityCounter.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.utils;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.Iterator;
 
@@ -37,7 +37,7 @@ public class CardinalityCounter implements Iterator<int[]>, Iterable<int[]> {
 
     public int[] next() {
         if (!hasNext())
-            throw new GATKException("CANNOT iterate past end!");
+            throw new ReviewedStingException("CANNOT iterate past end!");
 
         // Copy the assignment to be returned:
         int[] nextList = new int[valList.length];
diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
index 93537299f..9809bff0d 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLoc.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.utils;
 
 import net.sf.samtools.SAMRecord;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.ArrayList;
 import java.util.List;
@@ -163,9 +163,9 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable, Serializable
         return ! discontinuousP( that );
     }
 
-    public GenomeLoc merge( GenomeLoc that ) throws GATKException {
+    public GenomeLoc merge( GenomeLoc that ) throws ReviewedStingException {
         if (!(this.contiguousP(that))) {
-            throw new GATKException("The two genome loc's need to be contigous");
+            throw new ReviewedStingException("The two genome loc's need to be contigous");
         }
 
         return new GenomeLoc(getContig(), this.contigIndex,
@@ -173,9 +173,9 @@ public class GenomeLoc implements Comparable<GenomeLoc>, Cloneable, Serializable
                              Math.max( getStop(), that.getStop()) );
     }
 
-    public GenomeLoc intersect( GenomeLoc that ) throws GATKException {
+    public GenomeLoc intersect( GenomeLoc that ) throws ReviewedStingException {
         if (!(this.overlapsP(that))) {
-            throw new GATKException("GenomeLoc::intersect(): The two genome loc's need to overlap");
+            throw new ReviewedStingException("GenomeLoc::intersect(): The two genome loc's need to overlap");
         }
 
         return new GenomeLoc(getContig(), this.contigIndex,
diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
index d6530ade0..8f23ae6c7 100644
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocParser.java
@@ -42,7 +42,7 @@ import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
 import org.broadinstitute.sting.utils.bed.BedParser;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.interval.IntervalMergingRule;
 import org.broadinstitute.sting.utils.text.XReadLines;
@@ -428,10 +428,10 @@ public class GenomeLocParser {
     public static GenomeLoc createGenomeLoc(int contigIndex, final long start, final long stop) {
         checkSetup();
         if (start < 0) {
-            throw new GATKException("Bad start position " + start);
+            throw new ReviewedStingException("Bad start position " + start);
         }
         if (stop < -1) {
-            throw new GATKException("Bad stop position " + stop);
+            throw new ReviewedStingException("Bad stop position " + stop);
         }    // a negative -1 indicates it's not a meaningful end position
 
 
@@ -498,16 +498,16 @@ public class GenomeLocParser {
      */
     private static GenomeLoc exceptionOnInvalidGenomeLoc(GenomeLoc toReturn) {
         if (toReturn.getStart() < 0) {
-            throw new GATKException("Parameters to GenomeLocParser are incorrect: the start position is less than 0");
+            throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the start position is less than 0");
         }
         if ((toReturn.getStop() != -1) && (toReturn.getStop() < 0)) {
-            throw new GATKException("Parameters to GenomeLocParser are incorrect: the stop position is less than 0");
+            throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the stop position is less than 0");
         }
         if (toReturn.getContigIndex() < 0) {
-            throw new GATKException("Parameters to GenomeLocParser are incorrect: the contig index is less than 0");
+            throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the contig index is less than 0");
         }
         if (toReturn.getContigIndex() >= contigInfo.getSequences().size()) {
-            throw new GATKException("Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count");
+            throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the contig index is greater then the stored sequence count");
 
         }
         return toReturn;
@@ -528,11 +528,11 @@ public class GenomeLocParser {
     private static void exceptionOnInvalidGenomeLocBounds(GenomeLoc locus) {
         int contigSize = contigInfo.getSequence(locus.getContigIndex()).getSequenceLength();
         if(locus.getStart() > contigSize)
-            throw new GATKException(String.format("GenomeLoc is invalid: locus start %d is after the end of contig %s",locus.getStart(),locus.getContig()));
+            throw new ReviewedStingException(String.format("GenomeLoc is invalid: locus start %d is after the end of contig %s",locus.getStart(),locus.getContig()));
         if(locus.getStop() > contigSize)
-            throw new GATKException(String.format("GenomeLoc is invalid: locus stop %d is after the end of contig %s",locus.getStop(),locus.getContig()));
+            throw new ReviewedStingException(String.format("GenomeLoc is invalid: locus stop %d is after the end of contig %s",locus.getStop(),locus.getContig()));
         if (locus.getStart() > locus.getStop()) {
-            throw new GATKException("Parameters to GenomeLocParser are incorrect: the start position is greater than the end position");
+            throw new ReviewedStingException("Parameters to GenomeLocParser are incorrect: the start position is greater than the end position");
         }
     }
 
@@ -624,7 +624,7 @@ public class GenomeLocParser {
 
         int index = -1;
         if ((index = contigInfo.getSequenceIndex(contig)) < 0) {
-            throw new GATKException("Contig name ( " + contig + " ) not in the set sequence dictionary.");
+            throw new ReviewedStingException("Contig name ( " + contig + " ) not in the set sequence dictionary.");
         }
         return exceptionOnInvalidGenomeLoc(new GenomeLoc(contig, index, loc.start, loc.getStop()));
     }
@@ -637,7 +637,7 @@ public class GenomeLocParser {
     public static GenomeLoc setContigIndex(GenomeLoc loc, int contig) {
         checkSetup();
         if ((contig >= GenomeLocParser.contigInfo.getSequences().size()) || (contig < 0)) {
-            throw new GATKException("Contig index ( " + contig + " ) is not in the sequence dictionary set.");
+            throw new ReviewedStingException("Contig index ( " + contig + " ) is not in the sequence dictionary set.");
         }
         return exceptionOnInvalidGenomeLoc(new GenomeLoc(GenomeLocParser.contigInfo.getSequence(contig).getSequenceName(), contig, loc.start, loc.getStop()));
     }
@@ -710,7 +710,7 @@ public class GenomeLocParser {
     /** check to make sure that we've setup the contig information */
     private static void checkSetup() {
         if (contigInfo == null) {
-            throw new GATKException("The GenomeLocParser hasn't been setup with a contig sequence yet");
+            throw new ReviewedStingException("The GenomeLocParser hasn't been setup with a contig sequence yet");
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java b/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java
index 28b4aa98c..fcb73f1ce 100755
--- a/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java
+++ b/java/src/org/broadinstitute/sting/utils/GenomeLocSortedSet.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.utils;
 import net.sf.samtools.SAMSequenceDictionary;
 import net.sf.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.*;
 
@@ -110,7 +110,7 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
         } else {
             int loc = Collections.binarySearch(mArray,e);
             if (loc >= 0) {
-                throw new GATKException("Genome Loc Sorted Set already contains the GenomicLoc " + e.toString());
+                throw new ReviewedStingException("Genome Loc Sorted Set already contains the GenomicLoc " + e.toString());
             } else {
                 mArray.add((loc+1) * -1,e);
                 return true;
@@ -194,7 +194,7 @@ public class GenomeLocSortedSet extends AbstractSet<GenomeLoc> {
             } else if ( e.getStop() < p.getStart() ) {
                 toExclude.pop();                 // p starts after e stops, e is done
             } else {
-                throw new GATKException("BUG: unexpected condition: p=" + p + ", e=" + e);
+                throw new ReviewedStingException("BUG: unexpected condition: p=" + p + ", e=" + e);
             }
 
             if ( i++ % 10000 == 0 )
diff --git a/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java b/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java
index e45e883cb..9cf1b8c06 100644
--- a/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java
+++ b/java/src/org/broadinstitute/sting/utils/HeapSizeMonitor.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.utils;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.lang.management.ManagementFactory;
 import java.lang.management.MemoryMXBean;
@@ -42,7 +42,7 @@ public class HeapSizeMonitor {
             monitorThread.join();
         }
         catch(InterruptedException ex) {
-            throw new GATKException("Unable to connect to monitor thread");
+            throw new ReviewedStingException("Unable to connect to monitor thread");
         }
         monitorThread = null;        
     }
@@ -74,7 +74,7 @@ public class HeapSizeMonitor {
                     Thread.sleep(monitorFrequencyMillis);
                 }
                 catch(InterruptedException ex) {
-                    throw new GATKException("Unable to continue monitoring heap consumption",ex);
+                    throw new ReviewedStingException("Unable to continue monitoring heap consumption",ex);
                 }
             }
         }
diff --git a/java/src/org/broadinstitute/sting/utils/MalformedGenomeLocException.java b/java/src/org/broadinstitute/sting/utils/MalformedGenomeLocException.java
index a0d11d6c7..ce554397c 100644
--- a/java/src/org/broadinstitute/sting/utils/MalformedGenomeLocException.java
+++ b/java/src/org/broadinstitute/sting/utils/MalformedGenomeLocException.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.utils;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 /**
  * User: hanna
  * Date: Jun 2, 2009
@@ -19,7 +19,7 @@ import org.broadinstitute.sting.utils.exceptions.GATKException;
  * bad sequence id out of bounds, etc.
  */
 
-public class MalformedGenomeLocException extends GATKException {
+public class MalformedGenomeLocException extends ReviewedStingException {
     /**
      * Create a new MalformedGenomeLocException with the given message.  Does not preserve the existing stack trace.
      * @param message The message.
diff --git a/java/src/org/broadinstitute/sting/utils/PathUtils.java b/java/src/org/broadinstitute/sting/utils/PathUtils.java
index 2feb14484..47466be20 100755
--- a/java/src/org/broadinstitute/sting/utils/PathUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/PathUtils.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.utils;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.List;
 import java.util.ArrayList;
@@ -114,7 +114,7 @@ public class PathUtils {
         }
 
         if (dir.listFiles() == null) {
-            throw new GATKException("The volume '" + dir.getAbsolutePath() + "' could not be accessed.");
+            throw new ReviewedStingException("The volume '" + dir.getAbsolutePath() + "' could not be accessed.");
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java b/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java
index b1a4e3c8d..1cfe4b25f 100644
--- a/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java
+++ b/java/src/org/broadinstitute/sting/utils/ReservoirDownsampler.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.utils;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.*;
 
@@ -35,7 +35,7 @@ public class ReservoirDownsampler<T> {
      */
     public ReservoirDownsampler(final int maxElements) {
         if(maxElements < 0)
-            throw new GATKException("Unable to work with an negative size collection of elements");
+            throw new ReviewedStingException("Unable to work with an negative size collection of elements");
         this.reservoir = new ArrayList<T>(maxElements);
         this.maxElements = maxElements;
     }
diff --git a/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java b/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java
index 4198bc9c3..fb3d6f6a2 100755
--- a/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/SequenceDictionaryUtils.java
@@ -29,7 +29,7 @@ import net.sf.samtools.SAMSequenceRecord;
 import org.apache.log4j.Logger;
 import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
 import org.broadinstitute.sting.gatk.arguments.ValidationExclusion;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
 import java.util.*;
@@ -116,7 +116,7 @@ public class SequenceDictionaryUtils {
             case OUT_OF_ORDER:
                 throw new UserException.IncompatibleSequenceDictionaries("Order of contigs differences, which is unsafe", name1, dict1, name2, dict2);
             default:
-                throw new GATKException("Unexpected SequenceDictionaryComparison type");
+                throw new ReviewedStingException("Unexpected SequenceDictionaryComparison type");
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java b/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java
index e5819fb75..b9ea9d0bc 100755
--- a/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java
+++ b/java/src/org/broadinstitute/sting/utils/WilcoxonRankSum.java
@@ -30,7 +30,7 @@ import cern.jet.random.Normal;
 import java.util.*;
 
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 public class WilcoxonRankSum {
     static final String headerString = ("nA nB .005 .01 .025 .05 .10 .20");
@@ -186,7 +186,7 @@ public class WilcoxonRankSum {
                 U = n1 < n2 ? U1 : U2;
                 break;
             default:
-                throw new GATKException("Unexpected WILCOXON H0: " + h0);
+                throw new ReviewedStingException("Unexpected WILCOXON H0: " + h0);
         }
 
         // data is nA nB then
@@ -233,7 +233,7 @@ public class WilcoxonRankSum {
                 pvalue = NORMAL.cdf(z);
                 break;
             default:
-                throw new GATKException("Unexpected WILCOXON H0: " + h0);
+                throw new ReviewedStingException("Unexpected WILCOXON H0: " + h0);
         }
 
         return pvalue;
diff --git a/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
index 905814304..9b7c2c4de 100755
--- a/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/classloader/JVMUtils.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.utils.classloader;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.lang.reflect.Modifier;
 import java.lang.reflect.Field;
@@ -126,7 +126,7 @@ public class JVMUtils {
             field.set(instance, value);
         }
         catch( IllegalAccessException ex ) {
-            throw new GATKException(String.format("Could not set %s in instance %s to %s",field.getName(),instance.getClass().getName(),value.toString()));
+            throw new ReviewedStingException(String.format("Could not set %s in instance %s to %s",field.getName(),instance.getClass().getName(),value.toString()));
         }
     }
 
@@ -142,7 +142,7 @@ public class JVMUtils {
             return field.get(instance);
         }
         catch( IllegalAccessException ex ) {
-            throw new GATKException(String.format("Could not retrieve %s in instance %s",field.getName(),instance.getClass().getName()));
+            throw new ReviewedStingException(String.format("Could not retrieve %s in instance %s",field.getName(),instance.getClass().getName()));
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
index b97dff22c..4f570aa7a 100755
--- a/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/classloader/PackageUtils.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.classloader;
 
 import ch.qos.logback.classic.Level;
 import ch.qos.logback.classic.Logger;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 import org.reflections.Reflections;
 import org.reflections.scanners.SubTypesScanner;
@@ -136,7 +136,7 @@ public class PackageUtils {
           method.invoke(ClassLoader.getSystemClassLoader(), url);
           resetReflections();
       } catch (Exception e) {
-          throw new GATKException("Error adding url to the current classloader.", e);
+          throw new ReviewedStingException("Error adding url to the current classloader.", e);
       }
     }
 
diff --git a/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java b/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java
index 4d59f9400..bc26a0609 100644
--- a/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java
+++ b/java/src/org/broadinstitute/sting/utils/classloader/PluginManager.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.utils.classloader;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.DynamicClassResolutionException;
 
 import java.util.HashMap;
@@ -87,7 +87,7 @@ public abstract class PluginManager<PluginType> {
         Class<? extends PluginType> plugin = pluginsByName.get(pluginName);
         try {
             if( plugin == null )
-                throw new GATKException(String.format("Could not find %s with name: %s", pluginCategory,pluginName));
+                throw new ReviewedStingException(String.format("Could not find %s with name: %s", pluginCategory,pluginName));
             return plugin.newInstance();
         } catch (Exception e) {
             throw new DynamicClassResolutionException(plugin, e);
diff --git a/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java b/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java
index d107b85b2..5a669e65c 100644
--- a/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java
+++ b/java/src/org/broadinstitute/sting/utils/collections/CircularArray.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.utils.collections;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 
 /** This class, closely resembling a deque (except that it is not dynamically grown), 
@@ -69,7 +69,7 @@ public class CircularArray <T> {
 	
 	/** Creates an array of fixed length */
 	public CircularArray(int length) {
-		if ( length <= 0 ) throw new GATKException("CircularArray length must be positive. Passed: "+length);
+		if ( length <= 0 ) throw new ReviewedStingException("CircularArray length must be positive. Passed: "+length);
 		data = new Object[length]; 
 		offset = 0;
 	}
@@ -150,7 +150,7 @@ public class CircularArray <T> {
 		
 		/** Creates an array of fixed length */
 		public Int(int length) {
-			if ( length <= 0 ) throw new GATKException("CircularArray length must be positive. Passed: "+length);
+			if ( length <= 0 ) throw new ReviewedStingException("CircularArray length must be positive. Passed: "+length);
 			data = new int[length]; // automaticaly initialized to zeros
 			offset = 0;
 		}
diff --git a/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java b/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java
index c6bf96f64..61b842c05 100644
--- a/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java
+++ b/java/src/org/broadinstitute/sting/utils/collections/MergingIterator.java
@@ -27,7 +27,7 @@ package org.broadinstitute.sting.utils.collections;
 
 import org.broadinstitute.sting.gatk.refdata.utils.LocationAwareSeekableRODIterator;
 import org.broadinstitute.sting.gatk.refdata.utils.RODRecordList;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 
 import java.util.*;
@@ -42,10 +42,10 @@ public class MergingIterator implements Iterator<RODRecordList>, Iterable<RODRec
         public Element(Iterator<RODRecordList> it) {
             if ( it instanceof LocationAwareSeekableRODIterator) {
                 this.it = (LocationAwareSeekableRODIterator)it;
-                if ( ! it.hasNext() ) throw new GATKException("Iterator is empty");
+                if ( ! it.hasNext() ) throw new ReviewedStingException("Iterator is empty");
                 update();
             } else {
-                throw new GATKException("Iterator passed to MergingIterator is not LocationAwareSeekableRODIterator");
+                throw new ReviewedStingException("Iterator passed to MergingIterator is not LocationAwareSeekableRODIterator");
             }
         }
 
diff --git a/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java b/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java
index 27d6619cd..d2baa46c1 100644
--- a/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/duplicates/DupUtils.java
@@ -28,7 +28,7 @@ package org.broadinstitute.sting.utils.duplicates;
 import net.sf.samtools.SAMRecord;
 import org.broadinstitute.sting.utils.*;
 import org.broadinstitute.sting.utils.collections.Pair;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
 import org.broadinstitute.sting.utils.pileup.PileupElement;
 import org.broadinstitute.sting.utils.pileup.ReadBackedPileupImpl;
@@ -41,7 +41,7 @@ public class DupUtils {
         try {
             return (SAMRecord)read.clone();
         } catch ( CloneNotSupportedException e ) {
-            throw new GATKException("Unexpected Clone failure!");
+            throw new ReviewedStingException("Unexpected Clone failure!");
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/utils/exceptions/GATKException.java b/java/src/org/broadinstitute/sting/utils/exceptions/ReviewedStingException.java
similarity index 74%
rename from java/src/org/broadinstitute/sting/utils/exceptions/GATKException.java
rename to java/src/org/broadinstitute/sting/utils/exceptions/ReviewedStingException.java
index a71cb85a8..e1ff72ca1 100644
--- a/java/src/org/broadinstitute/sting/utils/exceptions/GATKException.java
+++ b/java/src/org/broadinstitute/sting/utils/exceptions/ReviewedStingException.java
@@ -24,17 +24,17 @@
 
 package org.broadinstitute.sting.utils.exceptions;
 
-import org.broadinstitute.sting.utils.exceptions.StingException;
-
 /**
- * Temp class to track split from Sting exception to UserException
+ * A trivial extension around StingException to mark exceptions that have been reviewed for correctness,
+ * completeness, etc.  By using this exception you are saying "this is the right error message".  StingException
+ * is now just a catch all for lazy users.
  */
-public class GATKException extends StingException {
-    public GATKException(String msg) {
+public class ReviewedStingException extends StingException {
+    public ReviewedStingException(String msg) {
         super(msg);
     }
 
-    public GATKException(String message, Throwable throwable) {
+    public ReviewedStingException(String message, Throwable throwable) {
         super(message, throwable);
     }
 }
diff --git a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
index b7fe6655f..b5cd705db 100755
--- a/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
+++ b/java/src/org/broadinstitute/sting/utils/exceptions/UserException.java
@@ -41,7 +41,7 @@ import java.util.Arrays;
  * Date: Sep 3, 2010
  * Time: 2:24:09 PM
  */
-public class UserException extends GATKException {
+public class UserException extends ReviewedStingException {
     public UserException(String msg) { super(msg); }
     public UserException(String msg, Throwable e) { super(msg, e); }
     private UserException(Throwable e) { super("", e); } // cannot be called, private access
diff --git a/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java b/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java
index 8b1e85030..90f9fe5bd 100644
--- a/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/fasta/ArtificialFastaUtils.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.utils.fasta;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.FileNotFoundException;
 import java.io.FileOutputStream;
@@ -34,7 +34,7 @@ public class ArtificialFastaUtils {
         try {
             s = new PrintStream(new FileOutputStream(fileName));
         } catch (FileNotFoundException e) {
-            throw new GATKException("Filename " + fileName + " passed to the ArtificialFastaUtils generated a FileNotFound exception", e);
+            throw new ReviewedStingException("Filename " + fileName + " passed to the ArtificialFastaUtils generated a FileNotFound exception", e);
         }
         generateFakeFasta(contigNames, contigSizes, pattern, s);
     }
@@ -58,7 +58,7 @@ public class ArtificialFastaUtils {
      */
     private static void generateFakeFasta(List<String> contigNames, List<Integer> contigSizes, BASE_PATTERN pattern, PrintStream s) {
         if (contigNames.size() != contigSizes.size()) {
-            throw new GATKException("ArtificialContig name and size arrays are not equal sizes");
+            throw new ReviewedStingException("ArtificialContig name and size arrays are not equal sizes");
         }
         for (int x = 0; x < contigNames.size(); x++) {
             ArtificialContig tig = new ArtificialContig(contigNames.get(x), contigSizes.get(x), pattern);
@@ -122,7 +122,7 @@ class ArtificialContig {
             case ALL_G:
                 return "G";
             default:
-                throw new GATKException("Unknown base pattern");
+                throw new ReviewedStingException("Unknown base pattern");
         }
     }
 
diff --git a/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java b/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java
index 767a7aadf..965210bea 100644
--- a/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java
+++ b/java/src/org/broadinstitute/sting/utils/file/FSLockWithShared.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.utils.file;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.io.IOException;
@@ -143,7 +143,7 @@ public class FSLockWithShared {
                 channel.close();
         }
         catch (Exception e) {
-            throw new GATKException("An error occurred while unlocking file", e);
+            throw new ReviewedStingException("An error occurred while unlocking file", e);
         }
     }
 }
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java b/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java
index 334394a3e..f68523479 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/LikelihoodObject.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.utils.genotype;
 import edu.mit.broad.picard.genotype.DiploidGenotype;
 import edu.mit.broad.picard.genotype.geli.GenotypeLikelihoods;
 import net.sf.samtools.SAMFileHeader;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.HashMap;
 
@@ -234,15 +234,15 @@ public class LikelihoodObject {
         switch (mLikelihoodType) {
             case NEGATIVE_LOG:
                 if (score < 0)
-                    throw new GATKException("Likelikhood score of " + score + " is invalid, for NEGATIVE_LOG it must be greater than or equal to 0");
+                    throw new ReviewedStingException("Likelikhood score of " + score + " is invalid, for NEGATIVE_LOG it must be greater than or equal to 0");
                 break;
             case LOG:
                 if (score > 0)
-                    throw new GATKException("Likelikhood score of " + score + " is invalid, for LOG it must be less than or equal to 0");
+                    throw new ReviewedStingException("Likelikhood score of " + score + " is invalid, for LOG it must be less than or equal to 0");
                 break;
             case RAW:
                 if (score < 0 || score > 1)
-                    throw new GATKException("Likelikhood score of " + score + " is invalid, for RAW it must be [0,1]");
+                    throw new ReviewedStingException("Likelikhood score of " + score + " is invalid, for RAW it must be [0,1]");
                 break;
         }
     }
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java
index bf5b15d02..86c53fe99 100644
--- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFReader.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.utils.genotype.glf;
 import net.sf.samtools.util.BinaryCodec;
 import net.sf.samtools.util.BlockCompressedInputStream;
 import net.sf.samtools.util.RuntimeEOFException;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 import org.broadinstitute.sting.utils.genotype.LikelihoodObject;
 
@@ -225,7 +225,7 @@ public class GLFReader implements Iterator<GLFRecord> {
     }
 
     public void remove() {
-        throw new GATKException("GLFReader doesn't support remove()");
+        throw new ReviewedStingException("GLFReader doesn't support remove()");
     }
 
     public void close() {
diff --git a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java
index 5d2b8e5cf..242d3a092 100755
--- a/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java
+++ b/java/src/org/broadinstitute/sting/utils/genotype/glf/GLFRecord.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.utils.genotype.glf;
 
 import net.sf.samtools.util.BinaryCodec;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 
 /*
@@ -251,7 +251,7 @@ public abstract class GLFRecord {
      * @return the minimum value
      */
     protected static double findMin(double vals[]) {
-        if (vals.length < 1) throw new GATKException("findMin: an array of size < 1 was passed in");
+        if (vals.length < 1) throw new ReviewedStingException("findMin: an array of size < 1 was passed in");
 
         double min = vals[0];
         for (double d : vals)
diff --git a/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java b/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java
index c2a5f8f77..b948b2eb5 100644
--- a/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java
+++ b/java/src/org/broadinstitute/sting/utils/help/ApplicationDetails.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.utils.help;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.commandline.CommandLineProgram;
 
@@ -80,7 +80,7 @@ public class ApplicationDetails {
             runningInstructions = JVMUtils.getLocationFor( application ).getName();
         }
         catch( IOException ex ) {
-            throw new GATKException("Unable to determine running instructions", ex);
+            throw new ReviewedStingException("Unable to determine running instructions", ex);
         }
 
         if( runningInstructions.endsWith(".jar") )
diff --git a/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
index b044f779a..49a93148b 100644
--- a/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
+++ b/java/src/org/broadinstitute/sting/utils/help/ResourceBundleExtractorDoclet.java
@@ -31,7 +31,7 @@ import java.util.*;
 import java.io.PrintStream;
 import java.io.IOException;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.classloader.JVMUtils;
 import org.broadinstitute.sting.utils.Utils;
 import org.broadinstitute.sting.gatk.walkers.Walker;
@@ -181,7 +181,7 @@ public class ResourceBundleExtractorDoclet {
         for(Tag tag: element.tags()) {
             if(tag.name().equals("@"+DisplayNameTaglet.NAME)) {
                 if(name != null)
-                    throw new GATKException("Only one display name tag can be used per package / walker.");
+                    throw new ReviewedStingException("Only one display name tag can be used per package / walker.");
                 name = tag.text();
             }
             else if(tag.name().equals("@"+VERSION_TAGLET_NAME))
diff --git a/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java b/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java
index 2eaa07d89..d5c47bc07 100644
--- a/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java
+++ b/java/src/org/broadinstitute/sting/utils/instrumentation/Sizeof.java
@@ -24,7 +24,7 @@
 
 package org.broadinstitute.sting.utils.instrumentation;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.lang.instrument.Instrumentation;
 import java.lang.reflect.Field;
@@ -73,7 +73,7 @@ public class Sizeof {
      */
     public static long getObjectSize(Object o) {
         if(!isEnabled())
-            throw new GATKException("Sizeof operator is currently disabled!  To enable, review the documentation in Sizeof.java");
+            throw new ReviewedStingException("Sizeof operator is currently disabled!  To enable, review the documentation in Sizeof.java");
         return instrumentation.getObjectSize(o);
     }
 
@@ -84,7 +84,7 @@ public class Sizeof {
      */
     public static long getObjectGraphSize(Object o) {
         if(!isEnabled())
-            throw new GATKException("Sizeof operator is currently disabled!  To enable, review the documentation in Sizeof.java");
+            throw new ReviewedStingException("Sizeof operator is currently disabled!  To enable, review the documentation in Sizeof.java");
         IdentityHashMap<Object,Object> objectsSeen = new IdentityHashMap<Object,Object>();
         return getObjectGraphSize(o,objectsSeen);
     }
@@ -134,7 +134,7 @@ public class Sizeof {
                     fieldValue = field.get(o);
                 }
                 catch(IllegalAccessException ex) {
-                    throw new GATKException("Unable to access field " + field.getName(),ex);
+                    throw new ReviewedStingException("Unable to access field " + field.getName(),ex);
                 }
                 totalSize += getObjectGraphSize(fieldValue,objectsSeen);
             }
diff --git a/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java b/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
index 7b039608f..95f1e3073 100644
--- a/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
+++ b/java/src/org/broadinstitute/sting/utils/pileup/AbstractReadBackedPileup.java
@@ -24,7 +24,7 @@
 
 package org.broadinstitute.sting.utils.pileup;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.BaseUtils;
 import org.broadinstitute.sting.gatk.iterators.IterableIterator;
@@ -82,8 +82,8 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
      *
      */
     public AbstractReadBackedPileup(GenomeLoc loc, List<PE> pileup) {
-        if ( loc == null ) throw new GATKException("Illegal null genomeloc in ReadBackedPileup");
-        if ( pileup == null ) throw new GATKException("Illegal null pileup in ReadBackedPileup");
+        if ( loc == null ) throw new ReviewedStingException("Illegal null genomeloc in ReadBackedPileup");
+        if ( pileup == null ) throw new ReviewedStingException("Illegal null pileup in ReadBackedPileup");
 
         this.loc = loc;
         this.pileupElementTracker = new UnifiedPileupElementTracker<PE>(pileup);
@@ -96,8 +96,8 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
      * @param pileup
      */
     public AbstractReadBackedPileup(GenomeLoc loc, List<PE> pileup, int size, int nDeletions, int nMQ0Reads) {
-        if ( loc == null ) throw new GATKException("Illegal null genomeloc in UnifiedReadBackedPileup");
-        if ( pileup == null ) throw new GATKException("Illegal null pileup in UnifiedReadBackedPileup");
+        if ( loc == null ) throw new ReviewedStingException("Illegal null genomeloc in UnifiedReadBackedPileup");
+        if ( pileup == null ) throw new ReviewedStingException("Illegal null pileup in UnifiedReadBackedPileup");
 
         this.loc = loc;
         this.pileupElementTracker = new UnifiedPileupElementTracker<PE>(pileup);
@@ -158,9 +158,9 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
      * @return
      */
     private PileupElementTracker<PE> readsOffsets2Pileup(List<SAMRecord> reads, List<Integer> offsets ) {
-        if ( reads == null ) throw new GATKException("Illegal null read list in UnifiedReadBackedPileup");
-        if ( offsets == null ) throw new GATKException("Illegal null offsets list in UnifiedReadBackedPileup");
-        if ( reads.size() != offsets.size() ) throw new GATKException("Reads and offset lists have different sizes!");
+        if ( reads == null ) throw new ReviewedStingException("Illegal null read list in UnifiedReadBackedPileup");
+        if ( offsets == null ) throw new ReviewedStingException("Illegal null offsets list in UnifiedReadBackedPileup");
+        if ( reads.size() != offsets.size() ) throw new ReviewedStingException("Reads and offset lists have different sizes!");
 
         UnifiedPileupElementTracker<PE> pileup = new UnifiedPileupElementTracker<PE>();
         for ( int i = 0; i < reads.size(); i++ ) {
@@ -178,8 +178,8 @@ public abstract class AbstractReadBackedPileup<RBP extends AbstractReadBackedPil
      * @return
      */
     private PileupElementTracker<PE> readsOffsets2Pileup(List<SAMRecord> reads, int offset ) {
-        if ( reads == null ) throw new GATKException("Illegal null read list in UnifiedReadBackedPileup");
-        if ( offset < 0 ) throw new GATKException("Illegal offset < 0 UnifiedReadBackedPileup");
+        if ( reads == null ) throw new ReviewedStingException("Illegal null read list in UnifiedReadBackedPileup");
+        if ( offset < 0 ) throw new ReviewedStingException("Illegal offset < 0 UnifiedReadBackedPileup");
 
         UnifiedPileupElementTracker<PE> pileup = new UnifiedPileupElementTracker<PE>();
         for ( int i = 0; i < reads.size(); i++ ) {
diff --git a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
index 42718320e..b64ef8ce0 100644
--- a/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
+++ b/java/src/org/broadinstitute/sting/utils/pileup/ReadBackedExtendedEventPileupImpl.java
@@ -23,7 +23,7 @@
  */
 package org.broadinstitute.sting.utils.pileup;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.collections.Pair;
 
@@ -140,7 +140,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<
                 case INSERTION: v[i] = 'I'; break;
                 case DELETION: v[i] = 'D'; break;
                 case NOEVENT: v[i] = '.'; break;
-                default: throw new GATKException("Unknown event type encountered: "+e.getType());
+                default: throw new ReviewedStingException("Unknown event type encountered: "+e.getType());
             }
             i++;
         }
@@ -190,7 +190,7 @@ public class ReadBackedExtendedEventPileupImpl extends AbstractReadBackedPileup<
                     indel = getDeletionString(e.getEventLength(),refBases);
                     break;
                 case NOEVENT: continue;
-                default: throw new GATKException("Unknown event type encountered: "+e.getType());
+                default: throw new ReviewedStingException("Unknown event type encountered: "+e.getType());
             }
 
             cnt = events.get(indel);
diff --git a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
index 6683c89d2..c4f3338f0 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/AlignmentUtils.java
@@ -31,7 +31,7 @@ import net.sf.samtools.Cigar;
 import net.sf.samtools.CigarElement;
 import net.sf.samtools.util.StringUtil;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.pileup.*;
 import org.broadinstitute.sting.utils.Utils;
 
@@ -146,7 +146,7 @@ public class AlignmentUtils {
                 case H:
                 case P:
                     break;
-                default: throw new GATKException("The " + ce.getOperator() + " cigar element is not currently supported");
+                default: throw new ReviewedStingException("The " + ce.getOperator() + " cigar element is not currently supported");
             }
 
         }
@@ -298,7 +298,7 @@ public class AlignmentUtils {
             case P:
                 break;
             default:
-                throw new GATKException( "Unsupported cigar operator: " + ce.getOperator() );
+                throw new ReviewedStingException( "Unsupported cigar operator: " + ce.getOperator() );
             }
         }
         return alignment;
@@ -337,7 +337,7 @@ public class AlignmentUtils {
             case P:
                 break;
             default:
-                throw new GATKException( "Unsupported cigar operator: " + ce.getOperator() );
+                throw new ReviewedStingException( "Unsupported cigar operator: " + ce.getOperator() );
             }
         }
         return alignment;
diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java
index 5297e0345..16293ba62 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMFileReader.java
@@ -10,7 +10,7 @@ import java.io.ByteArrayInputStream;
 import java.io.UnsupportedEncodingException;
 import java.util.*;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 /**
@@ -93,7 +93,7 @@ public class ArtificialSAMFileReader extends SAMFileReader {
             return new ByteArrayInputStream(byteArray);
         }
         catch( UnsupportedEncodingException ex ) {
-            throw new GATKException("Unable to build empty input stream",ex);
+            throw new ReviewedStingException("Unable to build empty input stream",ex);
         }
     }
 }
diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java
index d98a6c6f1..4f5dcca61 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMQueryIterator.java
@@ -6,7 +6,7 @@ import net.sf.samtools.SAMRecord;
 
 import java.util.List;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 
 /*
@@ -126,7 +126,7 @@ public class ArtificialSAMQueryIterator extends ArtificialSAMIterator {
         // sanity check that we have an actual matching read next
         SAMRecord rec = this.peek();
         if (rec == null) {
-            throw new GATKException("The next read doesn't match");
+            throw new ReviewedStingException("The next read doesn't match");
         }
         // set the seeked variable to true
         seeked = true;
@@ -165,7 +165,7 @@ public class ArtificialSAMQueryIterator extends ArtificialSAMIterator {
             super.next();
         }
         if (!super.hasNext()) {
-            throw new GATKException("Unable to find the target chromosome");
+            throw new ReviewedStingException("Unable to find the target chromosome");
         }
         while (super.hasNext() && this.peek().getAlignmentStart() < start) {
             super.next();
@@ -173,7 +173,7 @@ public class ArtificialSAMQueryIterator extends ArtificialSAMIterator {
         // sanity check that we have an actual matching read next
         SAMRecord rec = this.peek();
         if (!matches(rec)) {
-            throw new GATKException("The next read doesn't match");
+            throw new ReviewedStingException("The next read doesn't match");
         }
         // set the seeked variable to true
         seeked = true;
diff --git a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
index b424c59a3..095fe3ab3 100755
--- a/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/ArtificialSAMUtils.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.utils.sam;
 
 import net.sf.samtools.*;
 import org.broadinstitute.sting.gatk.iterators.StingSAMIterator;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.io.File;
 import java.util.ArrayList;
@@ -115,7 +115,7 @@ public class ArtificialSAMUtils {
      */
     public static SAMFileHeader createEnumeratedReadGroups( SAMFileHeader header, List<String> readGroupIDs, List<String> sampleNames ) {
         if (readGroupIDs.size() != sampleNames.size()) {
-            throw new GATKException("read group count and sample name count must be the same");
+            throw new ReviewedStingException("read group count and sample name count must be the same");
         }
 
         List<SAMReadGroupRecord> readGroups = new ArrayList<SAMReadGroupRecord>();
@@ -145,7 +145,7 @@ public class ArtificialSAMUtils {
     public static SAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, int length ) {
         if( (refIndex == SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart != SAMRecord.NO_ALIGNMENT_START) ||
             (refIndex != SAMRecord.NO_ALIGNMENT_REFERENCE_INDEX && alignmentStart == SAMRecord.NO_ALIGNMENT_START) )
-            throw new GATKException("Invalid alignment start for artificial read, start = " + alignmentStart);
+            throw new ReviewedStingException("Invalid alignment start for artificial read, start = " + alignmentStart);
         SAMRecord record = new SAMRecord(header);
         record.setReadName(name);
         record.setReferenceIndex(refIndex);
@@ -183,7 +183,7 @@ public class ArtificialSAMUtils {
      */
     public static SAMRecord createArtificialRead( SAMFileHeader header, String name, int refIndex, int alignmentStart, byte[] bases, byte[] qual ) {
         if (bases.length != qual.length) {
-            throw new GATKException("Passed in read string is different length then the quality array");
+            throw new ReviewedStingException("Passed in read string is different length then the quality array");
         }
         SAMRecord rec = createArtificialRead(header, name, refIndex, alignmentStart, bases.length);
         rec.setReadBases(bases);
diff --git a/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java b/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java
index ab22b4e19..f8a0ca6a7 100644
--- a/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java
+++ b/java/src/org/broadinstitute/sting/utils/sam/SAMFileReaderBuilder.java
@@ -29,7 +29,7 @@ import net.sf.samtools.SAMFileReader;
 
 import java.io.File;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 /**
  * Allows the user to steadily accumulate information about what
@@ -72,9 +72,9 @@ public class SAMFileReaderBuilder {
      */
     public SAMFileReader build() {
         if( samFile == null )
-            throw new GATKException( "Filename for output sam file must be supplied.");
+            throw new ReviewedStingException( "Filename for output sam file must be supplied.");
         if( validationStringency == null )
-            throw new GATKException( "Header for output sam file must be supplied.");
+            throw new ReviewedStingException( "Header for output sam file must be supplied.");
 
         SAMFileReader reader = new SAMFileReader( samFile );
         reader.setValidationStringency( validationStringency );
diff --git a/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java b/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java
index 93cece9cd..803d6ac0f 100644
--- a/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java
+++ b/java/src/org/broadinstitute/sting/utils/text/TextFormattingUtils.java
@@ -26,7 +26,7 @@
 package org.broadinstitute.sting.utils.text;
 
 import org.apache.log4j.Logger;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 
 import java.util.*;
 import java.util.regex.Pattern;
@@ -110,7 +110,7 @@ public class TextFormattingUtils {
                 bundle = new PropertyResourceBundle(new StringReader(""));
             }
             catch(IOException ioe) {
-                throw new GATKException("No resource bundle found, and unable to create an empty placeholder.",ioe);
+                throw new ReviewedStingException("No resource bundle found, and unable to create an empty placeholder.",ioe);
             }
         }
         return bundle;
diff --git a/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java b/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java
index 3c47d5a8b..ab91d0e2e 100755
--- a/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java
+++ b/java/src/org/broadinstitute/sting/utils/wiggle/WiggleWriter.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.utils.wiggle;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
@@ -76,7 +76,7 @@ public class WiggleWriter {
             write(wWriter,String.format("%d\t%s",loc.getStart(),dataPoint.toString()));
         } else {
             // todo -- maybe allow this to open a new file for the new chromosome?
-            throw new GATKException("Attempting to write multiple contigs into wiggle file, first contig was "+firstLoc.getContig()+" most recent "+loc.getContig());
+            throw new ReviewedStingException("Attempting to write multiple contigs into wiggle file, first contig was "+firstLoc.getContig()+" most recent "+loc.getContig());
         }
     }
 
diff --git a/java/test/org/broadinstitute/sting/BaseTest.java b/java/test/org/broadinstitute/sting/BaseTest.java
index 9f9f56676..1da296e42 100755
--- a/java/test/org/broadinstitute/sting/BaseTest.java
+++ b/java/test/org/broadinstitute/sting/BaseTest.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting;
 
 import org.apache.log4j.*;
 import org.apache.log4j.spi.LoggingEvent;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.junit.*;
 
 import java.io.*;
@@ -141,13 +141,13 @@ public abstract class BaseTest {
         try {
             digest = MessageDigest.getInstance("MD5");
         } catch (NoSuchAlgorithmException e) {
-            throw new GATKException("Unable to find MD5 digest");
+            throw new ReviewedStingException("Unable to find MD5 digest");
         }
         InputStream is;
         try {
             is = new FileInputStream(file);
         } catch (FileNotFoundException e) {
-            throw new GATKException("Unable to open file " + file);
+            throw new ReviewedStingException("Unable to open file " + file);
         }
         byte[] buffer = new byte[8192];
         int read;
@@ -161,14 +161,14 @@ public abstract class BaseTest {
 
         }
         catch (IOException e) {
-            throw new GATKException("Unable to process file for MD5", e);
+            throw new ReviewedStingException("Unable to process file for MD5", e);
         }
         finally {
             try {
                 is.close();
             }
             catch (IOException e) {
-                throw new GATKException("Unable to close input stream for MD5 calculation", e);
+                throw new ReviewedStingException("Unable to close input stream for MD5 calculation", e);
             }
         }
     }
diff --git a/java/test/org/broadinstitute/sting/WalkerTest.java b/java/test/org/broadinstitute/sting/WalkerTest.java
index d82a9d76d..fcd9ac2f0 100755
--- a/java/test/org/broadinstitute/sting/WalkerTest.java
+++ b/java/test/org/broadinstitute/sting/WalkerTest.java
@@ -28,7 +28,7 @@ package org.broadinstitute.sting;
 import junit.framework.Assert;
 import org.broadinstitute.sting.gatk.CommandLineExecutable;
 import org.broadinstitute.sting.gatk.CommandLineGATK;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.collections.Pair;
 import org.broadinstitute.sting.utils.Utils;
 import org.junit.Test;
@@ -62,7 +62,7 @@ public class WalkerTest extends BaseTest {
         if ( ! dir.exists() ) {
             System.out.printf("##### Creating MD5 db %s%n", MD5_FILE_DB_SUBDIR);
             if ( ! dir.mkdir() ) {
-                throw new GATKException("Infrastructure failure: failed to create md5 directory " + MD5_FILE_DB_SUBDIR);
+                throw new ReviewedStingException("Infrastructure failure: failed to create md5 directory " + MD5_FILE_DB_SUBDIR);
             }
         }
     }
@@ -81,7 +81,7 @@ public class WalkerTest extends BaseTest {
             try {
                 FileUtils.copyFile(resultsFile, dbFile);
             } catch ( IOException e ) {
-                throw new GATKException(e.getMessage());
+                throw new ReviewedStingException(e.getMessage());
             }
         } else {
             System.out.printf("##### MD5 file is up to date: %s%n", dbFile.getPath());
@@ -213,7 +213,7 @@ public class WalkerTest extends BaseTest {
         }
 
         public Class getExpectedException() {
-            if ( ! expectsException() ) throw new GATKException("Tried to get expection for walker test that doesn't expect one");
+            if ( ! expectsException() ) throw new ReviewedStingException("Tried to get expection for walker test that doesn't expect one");
             return expectedException;
         }
 
@@ -261,7 +261,7 @@ public class WalkerTest extends BaseTest {
             fl.deleteOnExit();
             return fl;
         } catch (IOException ex) {
-            throw new GATKException("Cannot create temp file: " + ex.getMessage(), ex);
+            throw new ReviewedStingException("Cannot create temp file: " + ex.getMessage(), ex);
         }
     }
 
diff --git a/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java b/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
index c2650aad1..833e6cce4 100755
--- a/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
+++ b/java/test/org/broadinstitute/sting/commandline/ParsingEngineUnitTest.java
@@ -26,7 +26,7 @@
 package org.broadinstitute.sting.commandline;
 
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.junit.Test;
 import org.junit.Before;
 import org.junit.Assert;
@@ -355,7 +355,7 @@ public class ParsingEngineUnitTest extends BaseTest {
         parsingEngine.validate();
     }
 
-    @Test(expected= GATKException.class)
+    @Test(expected= ReviewedStingException.class)
     public void duplicateLongNameTest() {
         parsingEngine.addArgumentSource( DuplicateLongNameProvider.class );
     }
@@ -368,7 +368,7 @@ public class ParsingEngineUnitTest extends BaseTest {
         public Integer bar;
     }
 
-    @Test(expected=GATKException.class)
+    @Test(expected= ReviewedStingException.class)
     public void duplicateShortNameTest() {
         parsingEngine.addArgumentSource( DuplicateShortNameProvider.class );
     }
@@ -593,7 +593,7 @@ public class ParsingEngineUnitTest extends BaseTest {
         RequiredArgProvider rap = new RequiredArgProvider();
     }
 
-    @Test(expected=GATKException.class)
+    @Test(expected= ReviewedStingException.class)
     public void multipleArgumentCollectionTest() {
         parsingEngine.addArgumentSource( MultipleArgumentCollectionProvider.class );
     }
diff --git a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java
index 23decfa06..691849959 100755
--- a/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/datasources/providers/ShardDataProviderUnitTest.java
@@ -1,6 +1,6 @@
 package org.broadinstitute.sting.gatk.datasources.providers;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.junit.Before;
 import org.junit.Assert;
 import org.junit.Test;
@@ -66,7 +66,7 @@ public class ShardDataProviderUnitTest extends BaseTest {
     /**
      * Try adding a view which conflicts with some other view that's already been registered.
      */
-    @Test(expected= GATKException.class)
+    @Test(expected= ReviewedStingException.class)
     public void testAddViewWithExistingConflict() {
         View initial = new ConflictingTestView( provider );
         View conflictsWithInitial = new TestView( provider );
@@ -75,7 +75,7 @@ public class ShardDataProviderUnitTest extends BaseTest {
     /**
      * Try adding a view which has a conflict with a previously registered view.
      */
-    @Test(expected=GATKException.class)
+    @Test(expected= ReviewedStingException.class)
     public void testAddViewWithNewConflict() {
         View conflictsWithInitial = new TestView( provider );
         View initial = new ConflictingTestView( provider );
diff --git a/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java b/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java
index fb2254e6d..0b86466dd 100644
--- a/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/filters/ReadGroupBlackListFilterUnitTest.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.gatk.filters;
 
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.junit.BeforeClass;
@@ -46,18 +46,18 @@ public class ReadGroupBlackListFilterUnitTest extends BaseTest {
         GenomeLocParser.setupRefContigOrdering(header.getSequenceDictionary());
     }
 
-    @Test(expected = GATKException.class)
+    @Test(expected = ReviewedStingException.class)
     public void testBadFilter() {
         List<String> badFilters = Collections.singletonList("bad");
         new ReadGroupBlackListFilter(badFilters);
     }
-    @Test(expected = GATKException.class)
+    @Test(expected = ReviewedStingException.class)
     public void testBadFilterTag() {
         List<String> badFilters = Collections.singletonList("bad:filter");
         new ReadGroupBlackListFilter(badFilters);
     }
 
-    @Test(expected = GATKException.class)
+    @Test(expected = ReviewedStingException.class)
     public void testBadFilterFile() {
         List<String> badFilters = Collections.singletonList("/foo/bar/rgbl.txt");
         new ReadGroupBlackListFilter(badFilters);
diff --git a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java
index 98807fba0..8e81d83f0 100644
--- a/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java
+++ b/java/test/org/broadinstitute/sting/gatk/refdata/tracks/RMDTrackManagerUnitTest.java
@@ -27,7 +27,7 @@ import net.sf.samtools.SAMSequenceRecord;
 import net.sf.picard.reference.IndexedFastaSequenceFile;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.refdata.utils.GATKFeature;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.junit.Assert;
 import org.junit.Before;
@@ -72,7 +72,7 @@ public class RMDTrackManagerUnitTest extends BaseTest {
             try {
                 fIter = ((TribbleTrack) t).query("1", 1, 5000);
             } catch (IOException e) {
-                throw new GATKException("blah I/O exception");
+                throw new ReviewedStingException("blah I/O exception");
             }
             while (fIter.hasNext()) {
                 fIter.next();
@@ -123,7 +123,7 @@ public class RMDTrackManagerUnitTest extends BaseTest {
                 try {
                     fIter = ((TribbleTrack) t).query("1", x, x + intervalSize);
                 } catch (IOException e) {
-                    throw new GATKException("blah I/O exception");
+                    throw new ReviewedStingException("blah I/O exception");
                 }
                 while (fIter.hasNext()) {
                     fIter.next();
diff --git a/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java b/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java
index 46b2ed6f2..293c37cdd 100644
--- a/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/GenomeLocParserUnitTest.java
@@ -3,7 +3,7 @@ package org.broadinstitute.sting.utils;
 
 import net.sf.samtools.SAMFileHeader;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 
 import static org.junit.Assert.assertEquals;
@@ -20,7 +20,7 @@ import org.junit.Test;
  *         Test out the functionality of the new genome loc parser
  */
 public class GenomeLocParserUnitTest extends BaseTest {
-    @Test(expected = GATKException.class)
+    @Test(expected = ReviewedStingException.class)
     public void testUnsetupException() {
         GenomeLocParser.contigInfo = null;
         GenomeLocParser.createGenomeLoc(0, 0, 0);
@@ -66,7 +66,7 @@ public class GenomeLocParserUnitTest extends BaseTest {
         assertEquals("chr1".compareTo(GenomeLocParser.getContigInfo("chr1").getSequenceName()), 0); // should be in the reference
     }
 
-    @Test(expected = GATKException.class)
+    @Test(expected = ReviewedStingException.class)
     public void testParseBadString() {
         GenomeLocParser.parseGenomeLoc("Bad:0-1");
     }
@@ -144,7 +144,7 @@ public class GenomeLocParserUnitTest extends BaseTest {
         assertEquals(1, loc.getStart());
     }
 
-    @Test(expected = GATKException.class)
+    @Test(expected = ReviewedStingException.class)
     public void testGenomeLocParseOnlyBadChrome() {
         GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr12");
         assertEquals(0, loc.getContigIndex());
@@ -152,7 +152,7 @@ public class GenomeLocParserUnitTest extends BaseTest {
         assertEquals(1, loc.getStart());
     }
 
-    @Test(expected = GATKException.class)
+    @Test(expected = ReviewedStingException.class)
     public void testGenomeLocBad() {
         GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1-");
         assertEquals(0, loc.getContigIndex());
@@ -160,7 +160,7 @@ public class GenomeLocParserUnitTest extends BaseTest {
         assertEquals(1, loc.getStart());
     }
 
-    @Test(expected = GATKException.class)
+    @Test(expected = ReviewedStingException.class)
     public void testGenomeLocBad2() {
         GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1-500-0");
         assertEquals(0, loc.getContigIndex());
@@ -168,7 +168,7 @@ public class GenomeLocParserUnitTest extends BaseTest {
         assertEquals(1, loc.getStart());
     }
 
-    @Test(expected = GATKException.class)
+    @Test(expected = ReviewedStingException.class)
     public void testGenomeLocBad3() {
         GenomeLoc loc = GenomeLocParser.parseGenomeLoc("chr1:1--0");
         assertEquals(0, loc.getContigIndex());
diff --git a/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java b/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java
index bbb11fc86..f722e1a42 100755
--- a/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/GenomeLocSortedSetUnitTest.java
@@ -2,7 +2,7 @@ package org.broadinstitute.sting.utils;
 
 import net.sf.samtools.SAMFileHeader;
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.sam.ArtificialSAMUtils;
 import static org.junit.Assert.assertTrue;
 import static org.junit.Assert.assertEquals;
@@ -81,7 +81,7 @@ public class GenomeLocSortedSetUnitTest extends BaseTest {
     }
 
 
-    @Test(expected = GATKException.class)
+    @Test(expected = ReviewedStingException.class)
     public void testAddDupplicate() {
         assertTrue(mSortedSet.size() == 0);
         GenomeLoc g = GenomeLocParser.createGenomeLoc(1, 0, 0);
diff --git a/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java b/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java
index f54944a05..88eea4604 100755
--- a/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/PathUtilsUnitTest.java
@@ -1,7 +1,7 @@
 package org.broadinstitute.sting.utils;
 
 import org.broadinstitute.sting.BaseTest;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.junit.Assert;
@@ -28,7 +28,7 @@ public class PathUtilsUnitTest extends BaseTest {
 
         try {
             PathUtils.refreshVolume(new File(filename));
-        } catch (GATKException e) {
+        } catch (ReviewedStingException e) {
             result = false;
         }
 
diff --git a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
index e22b5d18a..ab01ae5fc 100644
--- a/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/genotype/vcf/VCFWriterUnitTest.java
@@ -7,7 +7,7 @@ import org.broad.tribble.util.variantcontext.VariantContext;
 import org.broad.tribble.vcf.*;
 import org.broadinstitute.sting.BaseTest;
 import org.broadinstitute.sting.gatk.refdata.tracks.builders.TribbleRMDTrackBuilder;
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.junit.Assert;
@@ -58,7 +58,7 @@ public class VCFWriterUnitTest extends BaseTest {
              headerFromFile = (VCFHeader)reader.readHeader(lineReader);
         }
         catch (FileNotFoundException e ) {
-            throw new GATKException(e.getMessage());
+            throw new ReviewedStingException(e.getMessage());
         }
 
         int counter = 0;
@@ -80,7 +80,7 @@ public class VCFWriterUnitTest extends BaseTest {
             fakeVCFFile.delete();
         }
         catch (IOException e ) {
-            throw new GATKException(e.getMessage());
+            throw new ReviewedStingException(e.getMessage());
         }
 
     }
diff --git a/java/test/org/broadinstitute/sting/utils/interval/IntervalFileMergingIteratorUnitTest.java b/java/test/org/broadinstitute/sting/utils/interval/IntervalFileMergingIteratorUnitTest.java
index 9f94659f6..8c2bfa224 100644
--- a/java/test/org/broadinstitute/sting/utils/interval/IntervalFileMergingIteratorUnitTest.java
+++ b/java/test/org/broadinstitute/sting/utils/interval/IntervalFileMergingIteratorUnitTest.java
@@ -25,7 +25,7 @@
 
 package org.broadinstitute.sting.utils.interval;
 
-import org.broadinstitute.sting.utils.exceptions.GATKException;
+import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.junit.Assert;
@@ -101,7 +101,7 @@ public class IntervalFileMergingIteratorUnitTest extends BaseTest {
                     GenomeLoc l_expected = check_it.next();
 //                    System.out.println("int: "+l+" expected: "+l_expected) ;
                 }
-            } catch ( GATKException e) {
+            } catch ( ReviewedStingException e) {
                     Assert.assertEquals( e.getMessage(), "Interval chr5:7414 in the interval file is out of order.");
             }
         }