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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
This commit is contained in:
ebanks 2010-11-23 19:28:33 +00:00
parent fe28f8da9c
commit ea6e2218c1
2 changed files with 10 additions and 6 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/variantutils/LeftAlignVariants.java
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@ -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<Integer, Integer> {
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

8
java/src/org/broadinstitute/sting/playground/gatk/walkers/genotyper/UnifiedArgumentCollection.java
View File

@ -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;