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Merge pull request #443 from broadinstitute/eb_better_doc_for_minpruning 

Added docs for the minPruning argument in the HC
This commit is contained in:
Eric Banks 2013-12-05 08:52:56 -08:00
parent 623aaa0d6f e022db4690
commit 6d2fcd2df9
1 changed files with 7 additions and 0 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/HaplotypeCaller.java
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@ -335,6 +335,13 @@ public class HaplotypeCaller extends ActiveRegionWalker<List<VariantContext>, In
// general advanced arguments to control haplotype caller behavior // general advanced arguments to control haplotype caller behavior
// ----------------------------------------------------------------------------------------------- // -----------------------------------------------------------------------------------------------
/**
* Users should be aware that this argument can really affect the results of the variant calling and should exercise caution.
* Using a prune factor of 1 (or below) will prevent any pruning from the graph which is generally not ideal; it can make the
* calling much slower and even less accurate (because it can prevent effective merging of "tails" in the graph). Higher values
* tend to make the calling much faster, but also lowers the sensitivity of the results (because it ultimately requires higher
* depth to produce calls).
*/
@Advanced @Advanced
@Argument(fullName="minPruning", shortName="minPruning", doc = "The minimum allowed pruning factor in assembly graph. Paths with < X supporting kmers are pruned from the graph", required = false) @Argument(fullName="minPruning", shortName="minPruning", doc = "The minimum allowed pruning factor in assembly graph. Paths with < X supporting kmers are pruned from the graph", required = false)
protected int MIN_PRUNE_FACTOR = 2; protected int MIN_PRUNE_FACTOR = 2;