From 9e2522901436750a333b3600986fa13a0721fc5a Mon Sep 17 00:00:00 2001 From: ebanks Date: Mon, 22 Jun 2009 15:30:08 +0000 Subject: [PATCH] use better entropy threshold and don't print out "new" SNPs (since they're just an antrifact of the low (arbitrary) threshold git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1070 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/indels/IntervalCleanerWalker.java | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java index 2856605aa..1ebd55be3 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/indels/IntervalCleanerWalker.java @@ -32,7 +32,7 @@ public class IntervalCleanerWalker extends LocusWindowWalker @Argument(fullName="LODThresholdForCleaning", shortName="LOD", doc="LOD threshold above which the cleaner will clean", required=false) public double LOD_THRESHOLD = 5.0; @Argument(fullName="EntropyThreshold", shortName="entropy", doc="percentage of mismatches at a locus to be considered having high entropy", required=false) - public double MISMATCH_THRESHOLD = 0.25; + public double MISMATCH_THRESHOLD = 0.15; @Argument(fullName="maxConsensuses", shortName="maxConsensuses", doc="max alternate consensuses to try (necesary to improve performance in deep coverage)", required=false) public int MAX_CONSENSUSES = 30; @Argument(fullName="maxReadsForConsensuses", shortName="greedy", doc="max reads used for finding the alternate consensuses (necesary to improve performance in deep coverage)", required=false) @@ -607,10 +607,10 @@ public class IntervalCleanerWalker extends LocusWindowWalker sb.append(" SAME_SNP\n"); else sb.append(" NOT_SNP\n"); - } else if ( cleanedMismatchBases[i] > totalBases[i] * MISMATCH_THRESHOLD ) { - sb.append(reads.get(0).getRead().getReferenceName() + ":"); - sb.append(((int)leftmostIndex + i)); - sb.append(" NEW_SNP\n"); + //} else if ( cleanedMismatchBases[i] > totalBases[i] * MISMATCH_THRESHOLD ) { + // sb.append(reads.get(0).getRead().getReferenceName() + ":"); + // sb.append(((int)leftmostIndex + i)); + // sb.append(" NEW_SNP\n"); } } }