diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
index 278317da3..c60eceaa4 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/bqsr/BaseRecalibrator.java
@@ -366,9 +366,7 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
     }
 
     protected static int[] calculateIsIndel( final GATKSAMRecord read, final EventType mode ) {
-        final byte[] readBases = read.getReadBases();
-        final int[] indel = new int[readBases.length];
-        Arrays.fill(indel, 0);
+        final int[] indel = new int[read.getReadBases().length];
         int readPos = 0;
         for ( final CigarElement ce : read.getCigar().getCigarElements() ) {
             final int elementLength = ce.getLength();
@@ -383,21 +381,19 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
                 }
                 case D:
                 {
-                    final int index = ( read.getReadNegativeStrandFlag() ? readPos : ( readPos > 0 ? readPos - 1 : readPos ) );
-                    indel[index] = ( mode.equals(EventType.BASE_DELETION) ? 1 : 0 );
+                    final int index = ( read.getReadNegativeStrandFlag() ? readPos : readPos - 1 );
+                    updateIndel(indel, index, mode, EventType.BASE_DELETION);
                     break;
                 }
                 case I:
                 {
                     final boolean forwardStrandRead = !read.getReadNegativeStrandFlag();
                     if( forwardStrandRead ) {
-                        indel[(readPos > 0 ? readPos - 1 : readPos)] = ( mode.equals(EventType.BASE_INSERTION) ? 1 : 0 );
-                    }
-                    for (int iii = 0; iii < elementLength; iii++) {
-                        readPos++;
+                        updateIndel(indel, readPos - 1, mode, EventType.BASE_INSERTION);
                     }
+                    readPos += elementLength;
                     if( !forwardStrandRead ) {
-                        indel[(readPos < indel.length ? readPos : readPos - 1)] = ( mode.equals(EventType.BASE_INSERTION) ? 1 : 0 );
+                        updateIndel(indel, readPos, mode, EventType.BASE_INSERTION);
                     }
                     break;
                 }
@@ -412,6 +408,12 @@ public class BaseRecalibrator extends ReadWalker<Long, Long> implements NanoSche
         return indel;
     }
 
+    private static void updateIndel(final int[] indel, final int index, final EventType mode, final EventType requiredMode) {
+        if ( mode == requiredMode && index >= 0 && index < indel.length )
+            // protect ourselves from events at the start or end of the read (1D3M or 3M1D)
+            indel[index] = 1;
+    }
+
     protected static double[] calculateFractionalErrorArray( final int[] errorArray, final byte[] baqArray ) {
         if(errorArray.length != baqArray.length ) {
             throw new ReviewedStingException("Array length mismatch detected. Malformed read?");
diff --git a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
index 907046704..71c29fe0b 100644
--- a/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
+++ b/protected/java/test/org/broadinstitute/sting/gatk/walkers/bqsr/BQSRIntegrationTest.java
@@ -111,7 +111,7 @@ public class BQSRIntegrationTest extends WalkerTest {
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-10,200,000", "", "85a120b7d86b61597b86b9e93decbdfc")},
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA12873.454.SRP000031.2009_06.chr1.10_20mb.1RG.bam", "1:10,000,000-10,200,000", "", "5248dc49aec0323c74b496bb4928c73c")},
                 {new BQSRTest(b36KGReference, validationDataLocation + "originalQuals.1kg.chr1.1-1K.1RG.bam", "1:1-1,000", " -OQ", "cb52f267e0010f849f50b0bf1de474a1")},
-                {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "1425a5063ee757dbfc013df24e65a67a")},
+                {new BQSRTest(b36KGReference, validationDataLocation + "NA19240.chr1.BFAST.SOLID.bam", "1:10,000,000-20,000,000", " --solid_recal_mode REMOVE_REF_BIAS", "fb372d0a8fc41b01ced1adab31546850")},
                 {new BQSRTest(b36KGReference, privateTestDir + "NA19240.chr1.BFAST.SOLID.hasCSNoCall.bam", "1:50,000-80,000", " --solid_nocall_strategy LEAVE_READ_UNRECALIBRATED", "c1c3cda8caceed619d3d439c3990cd26")},
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:anyNameABCD,VCF " + privateTestDir + "vcfexample3.vcf", "c9953f020a65c1603a6d71aeeb1b95f3")},
                 {new BQSRTest(b36KGReference, validationDataLocation + "NA12892.SLX.SRP000031.2009_06.selected.1Mb.1RG.bam", "1:10,000,000-10,200,000", " -knownSites:bed " + validationDataLocation + "bqsrKnownTest.bed", "5bfff0c699345cca12a9b33acf95588f")},