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Fix docs for ReadBackedPhasing

This commit is contained in:
Eric Banks 2012-12-12 20:28:04 +00:00
parent bba63a3b0e
commit 62eaffdf0a
1 changed files with 3 additions and 0 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
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@ -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;