From 27808d336af0745500f050b4f8150eb2c9e4b3d2 Mon Sep 17 00:00:00 2001
From: Geraldine Van der Auwera <vdauwera@broadinstitute.org>
Date: Thu, 26 Sep 2013 13:13:53 -0400
Subject: [PATCH] Minor clarifications regarding ignoreFilter argument

---
 .../walkers/variantrecalibration/ApplyRecalibration.java     | 5 ++++-
 .../walkers/variantrecalibration/VariantRecalibrator.java    | 5 ++++-
 2 files changed, 8 insertions(+), 2 deletions(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
index 3ae68edab..314efe2a2 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/ApplyRecalibration.java
@@ -136,7 +136,10 @@ public class ApplyRecalibration extends RodWalker<Integer, Integer> implements T
     /////////////////////////////
     @Argument(fullName="ts_filter_level", shortName="ts_filter_level", doc="The truth sensitivity level at which to start filtering", required=false)
     protected double TS_FILTER_LEVEL = 99.0;
-    @Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified the variant recalibrator will use variants even if the specified filter name is marked in the input VCF file", required=false)
+    /**
+     * For this to work properly, the -ignoreFilter argument should also be applied to the VariantRecalibration command.
+     */
+    @Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified, the recalibration will be applied to variants marked as filtered by the specified filter name in the input VCF file", required=false)
     private String[] IGNORE_INPUT_FILTERS = null;
     @Argument(fullName="excludeFiltered", shortName="ef", doc="Don't output filtered loci after applying the recalibration", required=false)
     protected boolean EXCLUDE_FILTERED = false;
diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
index 5a8debc72..1ee02d10d 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
@@ -201,7 +201,10 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
      */
     @Argument(fullName="TStranche", shortName="tranche", doc="The levels of novel false discovery rate (FDR, implied by ti/tv) at which to slice the data. (in percent, that is 1.0 for 1 percent)", required=false)
     private double[] TS_TRANCHES = new double[] {100.0, 99.9, 99.0, 90.0};
-    @Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified the variant recalibrator will use variants even if the specified filter name is marked in the input VCF file", required=false)
+    /**
+     * For this to work properly, the -ignoreFilter argument should also be applied to the ApplyRecalibration command.
+     */
+    @Argument(fullName="ignore_filter", shortName="ignoreFilter", doc="If specified, the variant recalibrator will also use variants marked as filtered by the specified filter name in the input VCF file", required=false)
     private String[] IGNORE_INPUT_FILTERS = null;
     @Output(fullName="rscript_file", shortName="rscriptFile", doc="The output rscript file generated by the VQSR to aid in visualization of the input data and learned model", required=false, defaultToStdout=false)
     private File RSCRIPT_FILE = null;