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Merge pull request #1542 from broadinstitute/rhl_update_stand_call_conf_doc_1538 

Update stand_call_conf doc string
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Ron Levine 2017-01-06 20:42:56 -05:00 committed by GitHub
parent e86da63d04 ab4a9fa64f
commit 7447616766
1 changed files with 7 additions and 3 deletions
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protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/engine/arguments/GenotypeCalculationArgumentCollection.java
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@ -101,9 +101,13 @@ public class GenotypeCalculationArgumentCollection implements Cloneable{
public double heterozygosityStandardDeviation = 0.01; public double heterozygosityStandardDeviation = 0.01;
/** /**
* The minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. Only genotypes with * The minimum phred-scaled confidence threshold at which variants should be called. Only variant sites with QUAL equal
* confidence >= this threshold are emitted as called sites. A reasonable threshold is 30 for high-pass calling (this * or greater than this threshold will be called. Note that since version 3.7, we no longer differentiate high confidence
* is the default). * from low confidence calls at the calling step. The default call confidence threshold is set low intentionally to achieve
* high sensitivity, which will allow false positive calls as a side effect. Be sure to perform some kind of filtering after
* calling to reduce the amount of false positives in your final callset. Note that when HaplotypeCaller is used in GVCF mode
* (using either -ERC GVCF or -ERC BP_RESOLUTION) the call threshold is automatically set to zero. Call confidence thresholding
* will then be performed in the subsequent GenotypeGVCFs command.
*/ */
@Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be called", required = false) @Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be called", required = false)
public double STANDARD_CONFIDENCE_FOR_CALLING = 10.0; public double STANDARD_CONFIDENCE_FOR_CALLING = 10.0;