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Fixing UG argument docs

This commit is contained in:
Eric Banks 2012-06-12 09:46:16 -04:00
parent a4defdfb29
commit fec0bd5e11
1 changed files with 4 additions and 7 deletions
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11
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedArgumentCollection.java
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@ -65,18 +65,15 @@ public class UnifiedArgumentCollection {
/** /**
* The minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. Only genotypes with * The minimum phred-scaled Qscore threshold to separate high confidence from low confidence calls. Only genotypes with
* confidence >= this threshold are emitted as called sites. A reasonable threshold is 30 for high-pass calling (this * confidence >= this threshold are emitted as called sites. A reasonable threshold is 30 for high-pass calling (this
* is the default). Note that the confidence (QUAL) values for multi-sample low-pass (e.g. 4x per sample) calling might * is the default).
* be significantly smaller with the new EXACT model than with our older GRID_SEARCH model, as the latter tended to
* over-estimate the confidence; for low-pass calling we tend to use much smaller thresholds (e.g. 4).
*/ */
@Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites 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 = 30.0; public double STANDARD_CONFIDENCE_FOR_CALLING = 30.0;
/** /**
* the minimum phred-scaled Qscore threshold to emit low confidence calls. Genotypes with confidence >= this but less * This argument allows you to emit low quality calls as filtered records.
* than the calling threshold are emitted but marked as filtered.
*/ */
@Argument(fullName = "standard_min_confidence_threshold_for_emitting", shortName = "stand_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)", required = false) @Argument(fullName = "standard_min_confidence_threshold_for_emitting", shortName = "stand_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants should be emitted (and filtered with LowQual if less than the calling threshold)", required = false)
public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0; public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0;
/** /**