diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerBelowFrequencyWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerBelowFrequencyWalker.java index 72dd8b0fe..3a5c20580 100644 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerBelowFrequencyWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/poolseq/PowerBelowFrequencyWalker.java @@ -45,10 +45,10 @@ public class PowerBelowFrequencyWalker extends LocusWalker { int minMappingQuality = -1; @Argument(fullName="ignoreForwardReads",doc="Use the forward reads at a site. Defaults to true.", required = false) - boolean ignoreForwardReads = true; + boolean ignoreForwardReads = false; @Argument(fullName="ignoreReverseReads",doc="Use the reverse reads at a site. Defaults to true.", required = false) - boolean ignoreReverseReads = true; + boolean ignoreReverseReads = false; public void initialize() { if ( alleleFreq < 1 ) {