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changed default AF for Mutect2 tumor-only #5067

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Jul 31, 2018
Merged

changed default AF for Mutect2 tumor-only #5067

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2 changes: 1 addition & 1 deletion src/main/java/org/broadinstitute/hellbender/tools/walkers/mutect/M2ArgumentCollection.java
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Original file line number Diff line number Diff line change
Expand Up @@ -35,7 +35,7 @@ public class M2ArgumentCollection extends AssemblyBasedCallerArgumentCollection


public static final double DEFAULT_AF_FOR_TUMOR_ONLY_CALLING = 5e-8;
public static final double DEFAULT_AF_FOR_TUMOR_NORMAL_CALLING = 1e-5;
public static final double DEFAULT_AF_FOR_TUMOR_NORMAL_CALLING = 1e-6;

//TODO: HACK ALERT HACK ALERT HACK ALERT
//TODO: GATK4 does not yet have a way to tag inputs, eg -I:tumor tumor.bam -I:normal normal.bam,
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