diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java
index ed7c8fbb0..563794c8c 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/GenotypeAlleleCounts.java
@@ -599,7 +599,7 @@ public class GenotypeAlleleCounts implements Comparable<GenotypeAlleleCounts>, C
             }
             // It is guaranteed that at this point alleleIndex == nextIndex
             // thanks to the condition of the enclosing while: there must be at least one index of interest that
-            // it is present in remaning (nextRank,endRank] interval as otherwise endRank would be less than nextRank.
+            // is present in the remaining (nextRank,endRank] interval as otherwise endRank would be less than nextRank.
             dest[nextDestOffset++] = sortedAlleleCounts[nextSortedAlleleCountsOffset++];
             nextIndex++;
         }
@@ -756,7 +756,7 @@ public class GenotypeAlleleCounts implements Comparable<GenotypeAlleleCounts>, C
      * </p>
      *
      * <p>
-     *     If a sufficiently large array is provided as {@code dest}, this is used as the destination. Unecessary
+     *     If a sufficiently large array is provided as {@code dest}, this is used as the destination. Unnecessary
      *     positions at the back of the array are left untouched.
      * </p>
      *
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
index f1cf88f63..6b28a9fae 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/genotyper/afcalc/GeneralPloidyExactAFCalc.java
@@ -245,7 +245,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
                                                          final LinkedList<ExactACset> ACqueue,
                                                          final HashMap<ExactACcounts, ExactACset> indexesToACset) {
 
-        // compute likeihood in "set" of new set based on original likelihoods
+        // compute likelihood in "set" of new set based on original likelihoods
         final int numAlleles = set.getACcounts().getCounts().length;
         final int newPloidy = set.getACsum();
         final double log10LofK = computeLofK(set, originalPool, newGL, log10AlleleFrequencyPriors, numAlleles, originalPloidy, newGLPloidy);
@@ -358,7 +358,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
      * @param numAlleles                Number of alleles (including ref)
      * @param ploidy1                   Ploidy of original pool (combined)
      * @param ploidy2                   Ploidy of new pool
-     * @return                          log-likehood of requested conformation
+     * @return                          log-likelihood of requested conformation
      */
     private double computeLofK(final ExactACset set,
                                final CombinedPoolLikelihoods firstGLs,
@@ -441,7 +441,7 @@ public class GeneralPloidyExactAFCalc extends ExactAFCalc {
     }
 
     /**
-     * Small helper routine - is a particular AC conformationv vector valid? ie are all elements non-negative and sum to ploidy?
+     * Small helper routine - is a particular AC conformation vector valid? ie are all elements non-negative and sum to ploidy?
      * @param set                            AC conformation vector
      * @param ploidy                         Ploidy of set
      * @return                               Valid conformation
diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
index dbb285b55..74e9df0cd 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCaller.java
@@ -243,7 +243,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
     @Hidden
     @Advanced
     @Argument(fullName="heterogeneousKmerSizeResolution",shortName="hksr",doc="how to solve heterogeneous kmer situations using the fast method",required=false)
-    protected HeterogeneousKmerSizeResolution heterogeneousKmerSizeResultion = HeterogeneousKmerSizeResolution.COMBO_MIN;
+    protected HeterogeneousKmerSizeResolution heterogeneousKmerSizeResolution = HeterogeneousKmerSizeResolution.COMBO_MIN;
 
     @Output(fullName="graphOutput", shortName="graph", doc="File to which debug assembly graph information should be written", required = false, defaultToStdout = false)
     protected PrintStream graphWriter = null;
@@ -822,7 +822,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
             case PairHMM:
                 return new PairHMMLikelihoodCalculationEngine( (byte)gcpHMM, pairHMM, log10GlobalReadMismappingRate, noFpga, pcrErrorModel );
             case GraphBased:
-                return new GraphBasedLikelihoodCalculationEngine( (byte)gcpHMM,log10GlobalReadMismappingRate,heterogeneousKmerSizeResultion,SCAC.DEBUG,debugGraphTransformations);
+                return new GraphBasedLikelihoodCalculationEngine( (byte)gcpHMM,log10GlobalReadMismappingRate, heterogeneousKmerSizeResolution,SCAC.DEBUG,debugGraphTransformations);
             case Random:
                 return new RandomLikelihoodCalculationEngine();
             default:
@@ -931,7 +931,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         final AssemblyResultSet untrimmedAssemblyResult = assembleReads(originalActiveRegion, givenAlleles);
 
         final TreeSet<VariantContext> allVariationEvents = untrimmedAssemblyResult.getVariationEvents();
-        // TODO - line bellow might be unecessary : it might be that assemblyResult will always have those alleles anyway
+        // TODO - line bellow might be unnecessary : it might be that assemblyResult will always have those alleles anyway
         // TODO - so check and remove if that is the case:
         allVariationEvents.addAll(givenAlleles);
 
@@ -973,7 +973,7 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
         final List<Haplotype> haplotypes = assemblyResult.getHaplotypeList();
         final Map<String,List<GATKSAMRecord>> reads = splitReadsBySample( regionForGenotyping.getReads() );
 
-        // Calculate the likelihoods: CPU intesive part.
+        // Calculate the likelihoods: CPU intensive part.
         final ReadLikelihoods<Haplotype> readLikelihoods =
                 likelihoodCalculationEngine.computeReadLikelihoods(assemblyResult,samplesList,reads);