diff --git a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
index b72b20e0b..b59b550e1 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/report/GATKReportTable.java
@@ -296,6 +296,10 @@ public class GATKReportTable {
         return primaryKeyColumn.contains(primaryKey);
     }
 
+    public Collection<Object> getPrimaryKeys() {
+        return Collections.unmodifiableCollection(primaryKeyColumn);
+    }
+
     /**
      * Set the value for a given position in the table
      *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
new file mode 100755
index 000000000..e7a2f74e2
--- /dev/null
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycle.java
@@ -0,0 +1,162 @@
+package org.broadinstitute.sting.gatk.walkers.diagnostics;
+
+import net.sf.samtools.SAMReadGroupRecord;
+import org.broadinstitute.sting.commandline.Argument;
+import org.broadinstitute.sting.commandline.Output;
+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.report.GATKReport;
+import org.broadinstitute.sting.gatk.report.GATKReportTable;
+import org.broadinstitute.sting.gatk.walkers.LocusWalker;
+import org.broadinstitute.sting.utils.BaseUtils;
+import org.broadinstitute.sting.utils.QualityUtils;
+import org.broadinstitute.sting.utils.pileup.PileupElement;
+import org.broadinstitute.sting.utils.sam.GATKSAMRecord;
+
+import java.io.PrintStream;
+
+/**
+ * Computes the read error rate per position in read (in the original 5'->3' orientation that the read had coming off the machine)
+ *
+ * Emits a GATKReport containing readgroup, cycle, mismatches, counts, qual, and error rate for each read
+ * group in the input BAMs FOR ONLY THE FIRST OF PAIR READS.
+ *
+ * <h2>Input</h2>
+ *  <p>
+ *      Any number of BAM files
+ *  </p>
+ *
+ * <h2>Output</h2>
+ *  <p>
+ *      GATKReport containing readgroup, cycle, mismatches, counts, qual, and error rate.
+ *
+ *      For example, running this tool on the NA12878 data sets:
+ *
+ *      <pre>
+ *      ##:GATKReport.v0.2 ErrorRatePerCycle : The error rate per sequenced position in the reads
+ *      readgroup  cycle  mismatches  counts  qual  errorrate
+ *      20FUK.1        0          80   23368    25   3.47e-03
+ *      20FUK.1        1          40   23433    28   1.75e-03
+ *      20FUK.1        2          36   23453    28   1.58e-03
+ *      20FUK.1        3          26   23476    29   1.15e-03
+ *      20FUK.1        4          32   23495    29   1.40e-03
+ *      up to 101 cycles
+ *      20FUK.2        0          77   20886    24   3.73e-03
+ *      20FUK.2        1          28   20920    29   1.39e-03
+ *      20FUK.2        2          24   20931    29   1.19e-03
+ *      20FUK.2        3          30   20940    28   1.48e-03
+ *      20FUK.2        4          25   20948    29   1.24e-03
+ *      up to 101 cycles
+ *      20FUK.3        0          78   22038    24   3.58e-03
+ *      20FUK.3        1          40   22091    27   1.86e-03
+ *      20FUK.3        2          23   22108    30   1.09e-03
+ *      20FUK.3        3          36   22126    28   1.67e-03
+ *      </pre>
+ *  </p>
+ *
+ * <h2>Examples</h2>
+ *  <pre>
+ *    java
+ *      -jar GenomeAnalysisTK.jar
+ *      -T ErrorRatePerCycle
+ *      -I bundle/current/b37/NA12878.HiSeq.WGS.bwa.cleaned.recal.hg19.20.bam
+ *      -R bundle/current/b37/human_g1k_v37.fasta
+ *      -o example.gatkreport.txt
+ *  </pre>
+ *
+ * @author Kiran Garimella, Mark DePristo
+ */
+public class ErrorRatePerCycle extends LocusWalker<Integer, Integer> {
+    @Output PrintStream out;
+    @Argument(fullName="min_base_quality_score", shortName="mbq", doc="Minimum base quality required to consider a base for calling", required=false)
+    public Integer MIN_BASE_QUAL = 0;
+    @Argument(fullName="min_mapping_quality_score", shortName="mmq", doc="Minimum read mapping quality required to consider a read for calling", required=false)
+    public Integer MIN_MAPPING_QUAL = 20;
+
+    private GATKReport report;
+    private GATKReportTable table;
+    private final static String reportName = "ErrorRatePerCycle";
+    private final static String reportDescription = "The error rate per sequenced position in the reads";
+
+    /**
+     * Allows us to use multiple records for the key (read group x cycle)
+     */
+    private static class TableKey implements Comparable<TableKey> {
+        final String readGroup;
+        final int cycle;
+
+        private TableKey(final String readGroup, final int cycle) {
+            this.readGroup = readGroup;
+            this.cycle = cycle;
+        }
+
+        @Override
+        public int compareTo(final TableKey tableKey) {
+            final int scmp = readGroup.compareTo(tableKey.readGroup);
+            if ( scmp == 0 )
+                return Integer.valueOf(cycle).compareTo(tableKey.cycle);
+            else
+                return scmp;
+        }
+    }
+
+    public void initialize() {
+        report = new GATKReport();
+        report.addTable(reportName, reportDescription);
+        table = report.getTable(reportName);
+        table.addPrimaryKey("key", false);
+        table.addColumn("readgroup", 0);
+        table.addColumn("cycle", 0);
+        table.addColumn("mismatches", 0);
+        table.addColumn("counts", 0);
+        table.addColumn("qual", 0);
+        table.addColumn("errorrate", 0.0f, "%.2e");
+    }
+
+    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
+        for ( final PileupElement p : context.getBasePileup() ) {
+            final GATKSAMRecord read = p.getRead();
+            final int offset = p.getOffset();
+            final boolean firstOfPair = ! read.getReadPairedFlag() || read.getFirstOfPairFlag();
+
+            if ( firstOfPair && read.getMappingQuality() >= MIN_MAPPING_QUAL && p.getQual() >= MIN_BASE_QUAL ) {
+                final byte readBase = p.getBase();
+                final byte refBase = ref.getBase();
+                final int cycle = offset;
+
+                if ( BaseUtils.isRegularBase(readBase) && BaseUtils.isRegularBase(refBase) ) {
+                    final TableKey key = new TableKey(read.getReadGroup().getReadGroupId(), cycle);
+
+                    if ( ! table.containsKey(key) ) {
+                        table.set(key, "cycle", cycle);
+                        table.set(key, "readgroup", read.getReadGroup().getReadGroupId());
+                    }
+
+                    table.increment(key, "counts");
+                    if (readBase != refBase)
+                        table.increment(key, "mismatches");
+                }
+            }
+        }
+
+        return null;
+    }
+
+    public Integer reduceInit() { return null; }
+
+    public Integer reduce(Integer value, Integer sum) { return null; }
+
+    public void onTraversalDone(Integer sum) {
+        for ( final Object key : table.getPrimaryKeys() ) {
+            final int mismatches = (Integer)table.get(key, "mismatches");
+            final int count = (Integer)table.get(key, "counts");
+            final double errorRate = (mismatches + 1) / (1.0*(count + 1));
+            final int qual = QualityUtils.probToQual(1-errorRate, 0.0);
+            table.set(key, "qual", qual);
+            table.set(key, "errorrate", errorRate);
+        }
+
+        report.print(out);
+    }
+}
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
index d7a48d321..14985907d 100644
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/ReadGroupProperties.java
@@ -94,9 +94,6 @@ import java.util.Map;
  *
  * @author Mark DePristo
  */
-
-
-
 public class ReadGroupProperties extends ReadWalker<Integer, Integer> {
     @Output
     public PrintStream out;
diff --git a/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java b/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java
new file mode 100644
index 000000000..accb9c0cf
--- /dev/null
+++ b/public/java/test/org/broadinstitute/sting/gatk/walkers/diagnostics/ErrorRatePerCycleIntegrationTest.java
@@ -0,0 +1,41 @@
+/*
+ * Copyright (c) 2012, The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person
+ * obtaining a copy of this software and associated documentation
+ * files (the "Software"), to deal in the Software without
+ * restriction, including without limitation the rights to use,
+ * copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following
+ * conditions:
+ *
+ * The above copyright notice and this permission notice shall be
+ * included in all copies or substantial portions of the Software.
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+ * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
+ * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+ * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+ * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+ * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+ * OTHER DEALINGS IN THE SOFTWARE.
+ */
+
+package org.broadinstitute.sting.gatk.walkers.diagnostics;
+
+import org.broadinstitute.sting.WalkerTest;
+import org.testng.annotations.Test;
+
+import java.util.Arrays;
+
+public class ErrorRatePerCycleIntegrationTest extends WalkerTest {
+    @Test
+    public void basicTest() {
+        WalkerTestSpec spec = new WalkerTestSpec(
+                "-T ErrorRatePerCycle -R " + b37KGReference + " -I " + b37GoodBAM + " -L 20:10,000,000-10,100,000 -o %s",
+                1,
+                Arrays.asList("0cc212ecb6df300e321784039ff29f13"));
+        executeTest("ErrorRatePerCycle:", spec);
+    }
+}
\ No newline at end of file