diff --git a/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R b/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R
index fd301cd97..6c4dace1d 100644
--- a/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R
+++ b/public/R/scripts/org/broadinstitute/sting/utils/recalibration/BQSR.R
@@ -1,4 +1,5 @@
 library("ggplot2")
+library("tools") #For compactPDF in R 2.13+
 
 args <- commandArgs(TRUE)
 data <- read.csv(args[1])
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index 744a094c6..073f56707 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -58,14 +58,11 @@ import java.util.*;
  * to the desired level but also has the information necessary to pull out more variants for a higher sensitivity but a
  * slightly lower quality level.
  *
- * <p>
- * See <a href="http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration">the GATK wiki for a tutorial and example recalibration accuracy plots.</a>
- *
  * <h2>Input</h2>
  * <p>
  * The input raw variants to be recalibrated.
  * <p>
- * The recalibration table file in CSV format that was generated by the VariantRecalibrator walker.
+ * The recalibration table file in VCF format that was generated by the VariantRecalibrator walker.
  * <p>
  * The tranches file that was generated by the VariantRecalibrator walker.
  *
@@ -82,6 +79,7 @@ import java.util.*;
  *   --ts_filter_level 99.0 \
  *   -tranchesFile path/to/output.tranches \
  *   -recalFile path/to/output.recal \
+ *   -mode SNP \
  *   -o path/to/output.recalibrated.filtered.vcf
  * </pre>
  *
diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 2a424e15b..a2909d4ca 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -38,7 +38,6 @@ import org.broadinstitute.sting.utils.MathUtils;
 import org.broadinstitute.sting.utils.QualityUtils;
 import org.broadinstitute.sting.utils.R.RScriptExecutor;
 import org.broadinstitute.sting.utils.Utils;
-import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeader;
 import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLine;
 import org.broadinstitute.sting.utils.collections.ExpandingArrayList;
@@ -48,7 +47,6 @@ import org.broadinstitute.sting.utils.io.Resource;
 import org.broadinstitute.sting.utils.variantcontext.VariantContext;
 import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
 import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriter;
-import org.broadinstitute.sting.utils.variantcontext.writer.VariantContextWriterFactory;
 
 import java.io.File;
 import java.io.FileNotFoundException;
@@ -73,15 +71,9 @@ import java.util.*;
  * the log odds ratio of being a true variant versus being false under the trained Gaussian mixture model.
  *
  * <p>
- * NOTE: Please see our <a href="http://www.broadinstitute.org/gsa/wiki/index.php/Best_Practice_Variant_Detection_with_the_GATK_v3">best practices wiki page</a> for our recommendations on which annotations to use for specific project designs.
- *
- * <p>
  * NOTE: In order to create the model reporting plots Rscript needs to be in your environment PATH (this is the scripting version of R, not the interactive version).
  * See <a target="r-project" href="http://www.r-project.org">http://www.r-project.org</a> for more info on how to download and install R.
  *
- * <p>
- * See <a href="http://www.broadinstitute.org/gsa/wiki/index.php/Variant_quality_score_recalibration">the GATK wiki for a tutorial and example recalibration accuracy plots.</a>
- *
  * <h2>Input</h2>
  * <p>
  * The input raw variants to be recalibrated.
@@ -90,7 +82,7 @@ import java.util.*;
  *
  * <h2>Output</h2>
  * <p>
- * A recalibration table file in CSV format that is used by the ApplyRecalibration walker.
+ * A recalibration table file in VCF format that is used by the ApplyRecalibration walker.
  * <p>
  * A tranches file which shows various metrics of the recalibration callset as a function of making several slices through the data.
  *
@@ -102,8 +94,9 @@ import java.util.*;
  *   -input NA12878.HiSeq.WGS.bwa.cleaned.raw.subset.b37.vcf \
  *   -resource:hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf \
  *   -resource:omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf \
- *   -resource:dbsnp,known=true,training=false,truth=false,prior=8.0 dbsnp_132.b37.vcf \
- *   -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an MQ \
+ *   -resource:dbsnp,known=true,training=false,truth=false,prior=6.0 dbsnp_135.b37.vcf \
+ *   -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ -an InbreedingCoeff \
+ *   -mode SNP \
  *   -recalFile path/to/output.recal \
  *   -tranchesFile path/to/output.tranches \
  *   -rscriptFile path/to/output.plots.R
@@ -187,9 +180,6 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
     @Advanced
     @Argument(fullName = "trustAllPolymorphic", shortName = "allPoly", doc = "Trust that all the input training sets' unfiltered records contain only polymorphic sites to drastically speed up the computation.", required = false)
     protected Boolean TRUST_ALL_POLYMORPHIC = false;
-    //@Hidden
-    //@Argument(fullName = "projectConsensus", shortName = "projectConsensus", doc = "Perform 1000G project consensus. This implies an extra prior factor based on the individual participant callsets passed in with consensus=true rod binding tags.", required = false)
-    //protected Boolean PERFORM_PROJECT_CONSENSUS = false;
 
     /////////////////////////////
     // Private Member Variables
@@ -268,10 +258,6 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
                     // Loop through the training data sets and if they overlap this loci then update the prior and training status appropriately
                     dataManager.parseTrainingSets( tracker, context.getLocation(), vc, datum, TRUST_ALL_POLYMORPHIC );
                     double priorFactor = QualityUtils.qualToProb( datum.prior );
-                    //if( PERFORM_PROJECT_CONSENSUS ) { // BUGBUG: need to resurrect this functionality?
-                    //    final double consensusPrior = QualityUtils.qualToProb( 1.0 + 5.0 * datum.consensusCount );
-                    //    priorFactor = 1.0 - ((1.0 - priorFactor) * (1.0 - consensusPrior));
-                    //}
                     datum.prior = Math.log10( priorFactor ) - Math.log10( 1.0 - priorFactor );
 
                     mapList.add( datum );