From 1d67d07cf118ca74a8a8b7987c68c6a252b47c29 Mon Sep 17 00:00:00 2001
From: Mauricio Carneiro <carneiro@broadinstitute.org>
Date: Mon, 10 Jun 2013 15:17:40 -0400
Subject: [PATCH] better docs for Qualify Missing Intervals

now that it's available to the public, better give'em good docs!
---
 .../walkers/diagnostics/missing/QualifyMissingIntervals.java   | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
index cdcf32dcc..d0db3ef98 100644
--- a/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
+++ b/protected/java/src/org/broadinstitute/sting/gatk/walkers/diagnostics/missing/QualifyMissingIntervals.java
@@ -87,7 +87,7 @@ import java.util.List;
  *
  * <h3>Input</h3>
  * <p>
- *  A reference file
+ *  A reference file (for GC content), the input bam file (for base and mapping quality calculation), the missing intervals (in the -L), the baits/targets used to sequence (in the -targets) and a bed file with the coding sequence intervals of the genome (in the -cds)
  * </p>
  *
  * <h3>Output</h3>
@@ -100,6 +100,7 @@ import java.util.List;
  * java -Xmx2g -jar GenomeAnalysisTK.jar \
  *   -T QualifyMissingIntervals \
  *   -R ref.fasta \
+ *   -I input.bam \
  *   -o output.grp \
  *   -L input.intervals \
  *   -cds cds.intervals \