From 62eaffdf0a475888bec87771a3c1499b0bbce524 Mon Sep 17 00:00:00 2001
From: Eric Banks <ebanks@broadinstitute.org>
Date: Wed, 12 Dec 2012 20:28:04 +0000
Subject: [PATCH] Fix docs for ReadBackedPhasing

---
 .../sting/gatk/walkers/phasing/ReadBackedPhasing.java          | 3 +++
 1 file changed, 3 insertions(+)

diff --git a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
index eda43e6a5..7d848d0d4 100755
--- a/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
+++ b/public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
@@ -135,6 +135,9 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
     @Argument(fullName = "permitNoSampleOverlap", shortName = "permitNoSampleOverlap", doc = "Don't exit (just WARN) when the VCF and BAMs do not overlap in samples", required = false)
     private boolean permitNoSampleOverlap = false;
 
+    /**
+     * Important note: do not use this argument if your input data set is not already phased or it will cause the tool to skip over all heterozygous sites.
+     */
     @Argument(fullName = "respectPhaseInInput", shortName = "respectPhaseInInput", doc = "Will only phase genotypes in cases where the resulting output will necessarily be consistent with any existing phase (for example, from trios)", required = false)
     private boolean respectPhaseInInput = false;