diff --git a/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java b/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java index f883a134f..d3f44faa0 100755 --- a/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java +++ b/java/src/org/broadinstitute/sting/gatk/refdata/PooledEMSNPROD.java @@ -40,7 +40,7 @@ public class PooledEMSNPROD extends TabularROD implements SNPCallFromGenotypes { public double getMAF() { return Double.parseDouble(this.get("EM_alt_freq")); } public double getHeterozygosity() { return 2 * getMAF() * (1 - getMAF()); } public boolean isGenotype() { return false; } - public double getVariationConfidence() { return Double.parseDouble(this.get("discovery_lod")); } + public double getVariationConfidence() { return Double.parseDouble(this.get("lod")); } public double getConsensusConfidence() { return -1; } public List getGenotype() throws IllegalStateException { throw new IllegalStateException(); } public int getPloidy() throws IllegalStateException { return 2; }