From ea6e2218c11850c444aeef72da802b799bc2ce6c Mon Sep 17 00:00:00 2001 From: ebanks Date: Tue, 23 Nov 2010 19:28:33 +0000 Subject: [PATCH] 1. dbsnp has some massive indels which my left-aligner was barfing on because there isn't enough reference context; fixed. 2. Lower default calling threshold to Q30 for UGv2. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4722 348d0f76-0448-11de-a6fe-93d51630548a --- .../gatk/walkers/variantutils/LeftAlignVariants.java | 8 ++++++-- .../gatk/walkers/genotyper/UnifiedArgumentCollection.java | 8 ++++---- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java index 4e7bef808..41f522eea 100755 --- a/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java +++ b/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java @@ -42,7 +42,6 @@ import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker; import org.broadinstitute.sting.gatk.walkers.*; import org.broadinstitute.sting.utils.GenomeLoc; -import org.broadinstitute.sting.utils.GenomeLocParser; import org.broadinstitute.sting.utils.SampleUtils; import org.broadinstitute.sting.utils.sam.AlignmentUtils; import org.broadinstitute.sting.utils.vcf.VCFUtils; @@ -114,8 +113,13 @@ public class LeftAlignVariants extends RodWalker { else indelLength = vc.getAlternateAllele(0).length(); + if ( indelLength > 200 ) { + writer.add(vc, ref.getBase()); + return 0; + } + // create an indel haplotype - int originalIndex = (int)(ref.getLocus().getStart() - ref.getWindow().getStart()) + 1; + int originalIndex = ref.getLocus().getStart() - ref.getWindow().getStart() + 1; final byte[] originalIndel = makeHaplotype(vc, refSeq, originalIndex, indelLength); // create a CIGAR string to represent the event diff --git a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java index 8478b2d65..34dcd7d54 100755 --- a/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java +++ b/java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java @@ -52,16 +52,16 @@ public class UnifiedArgumentCollection { public boolean ALL_BASES_MODE = false; @Argument(fullName = "standard_min_confidence_threshold_for_calling", shortName = "stand_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be called", required = false) - public double STANDARD_CONFIDENCE_FOR_CALLING = 50.0; + public double STANDARD_CONFIDENCE_FOR_CALLING = 30.0; @Argument(fullName = "standard_min_confidence_threshold_for_emitting", shortName = "stand_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants not at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)", required = false) - public double STANDARD_CONFIDENCE_FOR_EMITTING = 50.0; + public double STANDARD_CONFIDENCE_FOR_EMITTING = 30.0; @Argument(fullName = "trigger_min_confidence_threshold_for_calling", shortName = "trig_call_conf", doc = "The minimum phred-scaled confidence threshold at which variants at 'trigger' track sites should be called", required = false) - public double TRIGGER_CONFIDENCE_FOR_CALLING = 50.0; + public double TRIGGER_CONFIDENCE_FOR_CALLING = 30.0; @Argument(fullName = "trigger_min_confidence_threshold_for_emitting", shortName = "trig_emit_conf", doc = "The minimum phred-scaled confidence threshold at which variants at 'trigger' track sites should be emitted (and filtered if less than the calling threshold)", required = false) - public double TRIGGER_CONFIDENCE_FOR_EMITTING = 50.0; + public double TRIGGER_CONFIDENCE_FOR_EMITTING = 30.0; @Argument(fullName = "noSLOD", shortName = "nsl", doc = "If provided, we will not calculate the SLOD", required = false) public boolean NO_SLOD = false;