diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
index 1f430548b..62f6ff5a6 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/IndelGenotypeLikelihoodsCalculationModel.java
@@ -157,10 +157,10 @@ public class IndelGenotypeLikelihoodsCalculationModel extends GenotypeLikelihood
                  GATKSAMRecord read = ReadUtils.hardClipAdaptorSequence(p.getRead());
                 if (read == null)
                     continue;     
-                if(ReadUtils.is454Read(read)) {
+         /*       if(ReadUtils.is454Read(read)) {
                     continue;
                 }
-
+            */
                 if (DEBUG && p.isIndel()) {
                     System.out.format("Read: %s, cigar: %s, aln start: %d, aln end: %d, p.len:%d, Type:%s, EventBases:%s\n",
                             read.getReadName(),read.getCigar().toString(),read.getAlignmentStart(),read.getAlignmentEnd(),
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
index e7b9cfa68..419ae694f 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/indels/PairHMMIndelErrorModel.java
@@ -105,6 +105,7 @@ public class PairHMMIndelErrorModel {
     private static final double MIN_GAP_CONT_PENALTY = 10.0;
     private static final double GAP_PENALTY_HRUN_STEP = 1.0; // each increase in hrun decreases gap penalty by this.
 
+    private static final double GOP_454_DELTA = 15.0; // lower gap penalty for 454 reads
 
     private boolean doViterbi = false;
 
@@ -771,10 +772,10 @@ public class PairHMMIndelErrorModel {
                 if (read == null)
                     continue;
 
-                if(ReadUtils.is454Read(read) && !getGapPenaltiesFromFile) {
+         /*       if(ReadUtils.is454Read(read) && !getGapPenaltiesFromFile) {
                     continue;
                 }
-
+            */
                 double[] recalQuals = null;
 
  /*
@@ -990,6 +991,10 @@ public class PairHMMIndelErrorModel {
                                }  else {
                                    currentContextGOP = Arrays.copyOfRange(gapOpenProbabilityMap.get(a), (int)indStart, (int)indStop);
                                    currentContextGCP = Arrays.copyOfRange(gapContProbabilityMap.get(a), (int)indStart, (int)indStop);
+                                   if(ReadUtils.is454Read(read)) {
+                                       for (int k=0; k <currentContextGOP.length; k++ )
+                                           currentContextGOP[k] += GOP_454_DELTA/10;
+                                   }
                                    readLikelihood = computeReadLikelihoodGivenHaplotypeAffineGaps(haplotypeBases, readBases, readQuals, currentContextGOP, currentContextGCP);
                                }
                             }