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Added more options to control RBP behavior; raised default RBP PQ threshold to 20

This commit is contained in:
Menachem Fromer 2013-01-09 14:44:22 -05:00
parent 6089a4bf62
commit 077ea8f30c
1 changed files with 1 additions and 1 deletions
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protected/java/src/org/broadinstitute/sting/gatk/walkers/phasing/ReadBackedPhasing.java
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@ -117,7 +117,7 @@ public class ReadBackedPhasing extends RodWalker<PhasingStatsAndOutput, PhasingS
protected Integer maxPhaseSites = 10; // 2^10 == 10^3 diploid haplotypes
@Argument(fullName = "phaseQualityThresh", shortName = "phaseThresh", doc = "The minimum phasing quality score required to output phasing", required = false)
protected Double phaseQualityThresh = 10.0; // PQ = 10.0 <=> P(error) = 10^(-10/10) = 0.1, P(correct) = 0.9
protected Double phaseQualityThresh = 20.0; // PQ = 20.0 <=> P(error) = 10^(-20/10) = 0.01, P(correct) = 0.99
@Hidden
@Argument(fullName = "variantStatsFilePrefix", shortName = "variantStats", doc = "The prefix of the VCF/phasing statistics files [For DEBUGGING purposes only - DO NOT USE!]", required = false)