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Fix docs for ReadBackedPhasing

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1 parent 126fdb1 commit 92f8bb1b2101358b7c9376099f596afd7ec1d6e4 @eitanbanks eitanbanks committed Dec 12, 2012
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3 public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
@@ -135,6 +135,9 @@
@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;

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