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HaplotypeCaller: Variants found on the same haplotype are now written out with phased genotypes. There are serious eval issues with MNPs so disabling them for now.

This commit is contained in:
Ryan Poplin 2012-03-29 09:41:29 -04:00
parent a0843f125e
commit 9684a2efb0
1 changed files with 1 additions and 1 deletions
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public/java/src/org/broadinstitute/sting/gatk/walkers/varianteval/evaluators/CompOverlap.java
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@ -19,7 +19,7 @@ import org.broadinstitute.sting.utils.variantcontext.VariantContext;
*/ */
@Analysis(description = "The overlap between eval and comp sites") @Analysis(description = "The overlap between eval and comp sites")
public class CompOverlap extends VariantEvaluator implements StandardEval { public class CompOverlap extends VariantEvaluator implements StandardEval {
@DataPoint(description = "number of eval SNP sites", format = "%d") @DataPoint(description = "number of eval variant sites", format = "%d")
long nEvalVariants = 0; long nEvalVariants = 0;
@DataPoint(description = "number of eval sites outside of comp sites", format = "%d") @DataPoint(description = "number of eval sites outside of comp sites", format = "%d")