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a) Minor changes to indel consensus scripts to better reflect good default values, b) Fixed up Mills/Devine codec so it always produces correct ref padded bases, and added option to VariantsToVCF to fix reference base

This commit is contained in:
Guillermo del Angel 2011-08-04 15:34:49 -04:00
parent 406982284c
commit a8eb8c27f0
2 changed files with 15 additions and 0 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantDataManager.java
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@ -240,6 +240,14 @@ public class VariantDataManager {
if( jitter && annotationKey.equalsIgnoreCase("HRUN") ) { // Integer valued annotations must be jittered a bit to work in this GMM
value += -0.25 + 0.5 * GenomeAnalysisEngine.getRandomGenerator().nextDouble();
}
if (vc.isIndel() && annotationKey.equalsIgnoreCase("QD")) {
// normalize QD by event length for indel case
int eventLength = Math.abs(vc.getAlternateAllele(0).getBaseString().length() - vc.getReference().getBaseString().length()); // ignore multi-allelic complication here for now
if (eventLength > 0) // sanity check
value /= (double)eventLength;
}
if( jitter && annotationKey.equalsIgnoreCase("HaplotypeScore") && MathUtils.compareDoubles(value, 0.0, 0.0001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
if( jitter && annotationKey.equalsIgnoreCase("FS") && MathUtils.compareDoubles(value, 0.0, 0.001) == 0 ) { value = -0.2 + 0.4*GenomeAnalysisEngine.getRandomGenerator().nextDouble(); }
} catch( Exception e ) {

7
public/java/src/org/broadinstitute/sting/gatk/walkers/variantutils/VariantsToVCF.java
View File

@ -67,6 +67,9 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
@Argument(fullName="sample", shortName="sample", doc="The sample name represented by the variant rod (for data like GELI with genotypes)", required=false)
protected String sampleName = null;
@Argument(fullName="fixRef", shortName="fixRef", doc="Fix common reference base in case there's an indel without padding", required=false)
protected boolean fixReferenceBase = false;
private Set<String> allowedGenotypeFormatStrings = new HashSet<String>();
private boolean wroteHeader = false;
@ -104,6 +107,10 @@ public class VariantsToVCF extends RodWalker<Integer, Integer> {
vc = VariantContext.modifyGenotypes(vc, genotypes);
}
// todo - fix me. This may not be the cleanest way to handle features what need correct indel padding
if (fixReferenceBase) {
vc = new VariantContext("Variant",vc.getChr(),vc.getStart(), vc.getEnd(), vc.getAlleles(), vc.getGenotypes(), vc.getNegLog10PError(), vc.getFilters(),vc.getAttributes(), ref.getBase());
}
writeRecord(vc, tracker, ref.getBase());
}