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1. Newest version of the joint estimation model. Faster than previous version and now qscores can get to be > 39.8 for hets. 

2. More sanity checks in annotations


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2119 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-11-23 17:05:50 +00:00
parent ee2abd30c4
commit 14bf6ce83c
3 changed files with 121 additions and 23 deletions
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8
java/src/org/broadinstitute/sting/gatk/walkers/annotator/AlleleBalance.java
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@ -99,7 +99,13 @@ public class AlleleBalance implements VariantAnnotation {
double[] posteriors = ((PosteriorsBacked)g).getPosteriors();
posteriors = MathUtils.normalizeFromLog10(posteriors);
weights.add(posteriors[bestGenotype.ordinal()]);
double weight = posteriors[bestGenotype.ordinal()];
// sanity check
if ( MathUtils.compareDoubles(weight, 0.0) == 0 )
continue;
weights.add(weight);
refBalances.add((double)refCount / (double)(refCount + altCount));
}

8
java/src/org/broadinstitute/sting/gatk/walkers/annotator/OnOffGenotype.java
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@ -103,7 +103,13 @@ public class OnOffGenotype implements VariantAnnotation {
double[] posteriors = ((PosteriorsBacked)g).getPosteriors();
posteriors = MathUtils.normalizeFromLog10(posteriors);
weights.add(posteriors[bestGenotype.ordinal()]);
double weight = posteriors[bestGenotype.ordinal()];
// sanity check
if ( MathUtils.compareDoubles(weight, 0.0) == 0 )
continue;
weights.add(weight);
onOffBalances.add((double)onCount / (double)totalCount);
}

128
java/src/org/broadinstitute/sting/gatk/walkers/genotyper/DiploidGenotypeCalculationModel.java
View File

@ -12,6 +12,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
// the GenotypeLikelihoods map
private HashMap<String, GenotypeLikelihoods> GLs = new HashMap<String, GenotypeLikelihoods>();
private HashMap<Character, AlleleFrequencyMatrix> AFMatrixMap = new HashMap<Character, AlleleFrequencyMatrix>();
private enum GenotypeType { REF, HET, HOM }
@ -26,10 +27,18 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
protected void initialize(char ref, HashMap<String, AlignmentContextBySample> contexts, StratifiedContext contextType) {
// initialize the GenotypeLikelihoods
GLs.clear();
AFMatrixMap.clear();
// for each alternate allele, create a new matrix
for ( char alt : BaseUtils.BASES ) {
if ( alt != ref )
AFMatrixMap.put(alt, new AlleleFrequencyMatrix(contexts.size()));
}
// use flat priors for GLs
DiploidGenotypePriors priors = new DiploidGenotypePriors();
int index = 0;
for ( String sample : contexts.keySet() ) {
AlignmentContextBySample context = contexts.get(sample);
ReadBackedPileup pileup = new ReadBackedPileup(ref, context.getContext(contextType));
@ -38,34 +47,33 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
GenotypeLikelihoods GL = new GenotypeLikelihoods(baseModel, priors, defaultPlatform);
GL.add(pileup, true);
GLs.put(sample, GL);
double[] posteriors = GL.getPosteriors();
// for each alternate allele, fill the matrix
for ( char alt : BaseUtils.BASES ) {
if ( alt != ref ) {
DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(ref);
DiploidGenotype hetGenotype = ref < alt ? DiploidGenotype.valueOf(String.valueOf(ref) + String.valueOf(alt)) : DiploidGenotype.valueOf(String.valueOf(alt) + String.valueOf(ref));
DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(alt);
AFMatrixMap.get(alt).setLikelihoods(posteriors[refGenotype.ordinal()], posteriors[hetGenotype.ordinal()], posteriors[homGenotype.ordinal()], index);
}
}
index++;
}
}
protected double computeLog10PofDgivenAFi(char ref, char alt, double f, HashMap<String, AlignmentContextBySample> contexts, StratifiedContext contextType) {
DiploidGenotype refGenotype = DiploidGenotype.createHomGenotype(ref);
DiploidGenotype hetGenotype = ref < alt ? DiploidGenotype.valueOf(String.valueOf(ref) + String.valueOf(alt)) : DiploidGenotype.valueOf(String.valueOf(alt) + String.valueOf(ref));
DiploidGenotype homGenotype = DiploidGenotype.createHomGenotype(alt);
double PofDgivenAFi = 0.0;
// *** note that this code assumes that allele frequencies are passed in IN ORDER from 0 to 2N
// for each sample
for ( GenotypeLikelihoods GL : GLs.values() ) {
AlleleFrequencyMatrix matrix = AFMatrixMap.get(alt);
double[] posteriors = GL.getPosteriors();
double[] allelePosteriors = new double[] { posteriors[refGenotype.ordinal()], posteriors[hetGenotype.ordinal()], posteriors[homGenotype.ordinal()] };
allelePosteriors = MathUtils.normalizeFromLog10(allelePosteriors);
// calculate the posterior weighted frequencies
double[] HWvalues = getHardyWeinbergValues(f);
double samplePofDgivenAFi = 0.0;
samplePofDgivenAFi += HWvalues[GenotypeType.REF.ordinal()] * allelePosteriors[GenotypeType.REF.ordinal()];
samplePofDgivenAFi += HWvalues[GenotypeType.HET.ordinal()] * allelePosteriors[GenotypeType.HET.ordinal()];
samplePofDgivenAFi += HWvalues[GenotypeType.HOM.ordinal()] * allelePosteriors[GenotypeType.HOM.ordinal()];
PofDgivenAFi += Math.log10(samplePofDgivenAFi);
}
return PofDgivenAFi;
// for any frequency other than zero, calculate the next greedy entry
if ( MathUtils.compareDoubles(f, 0.0) != 0 )
matrix.incrementFrequency();
return matrix.getLikelihoodsOfFrequency();
}
protected List<Genotype> makeGenotypeCalls(char ref, char alt, HashMap<String, AlignmentContextBySample> contexts, GenomeLoc loc) {
@ -98,4 +106,82 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
return calls;
}
protected class AlleleFrequencyMatrix {
private double[][] matrix;
private int[] indexes;
private int N;
private int frequency;
public AlleleFrequencyMatrix(int N) {
this.N = N;
frequency = 0;
matrix = new double[N][3];
indexes = new int[N];
for (int i = 0; i < N; i++)
indexes[i] = 0;
}
public void setLikelihoods(double AA, double AB, double BB, int index) {
matrix[index][GenotypeType.REF.ordinal()] = AA;
matrix[index][GenotypeType.HET.ordinal()] = AB;
matrix[index][GenotypeType.HOM.ordinal()] = BB;
}
public void incrementFrequency() {
if ( frequency == 2 * N )
throw new StingException("Frequency was incremented past N; how is this possible?");
frequency++;
double greedy = -1.0 * Double.MAX_VALUE;
int greedyIndex = -1;
for (int i = 0; i < N; i++) {
if ( indexes[i] == GenotypeType.HET.ordinal() ) {
if ( matrix[i][GenotypeType.HOM.ordinal()] - matrix[i][GenotypeType.HET.ordinal()] > greedy ) {
greedy = matrix[i][GenotypeType.HOM.ordinal()] - matrix[i][GenotypeType.HET.ordinal()];
greedyIndex = i;
}
}
else if ( indexes[i] == GenotypeType.REF.ordinal() ) {
if ( matrix[i][GenotypeType.HET.ordinal()] - matrix[i][GenotypeType.REF.ordinal()] > greedy ) {
greedy = matrix[i][GenotypeType.HET.ordinal()] - matrix[i][GenotypeType.REF.ordinal()];
greedyIndex = i;
}
// note that we currently don't bother with breaking ties between samples
// (which would be done by looking at the HOM_VAR value) because it's highly
// unlikely that a collision will both occur and that the difference will
// be significant at HOM_VAR...
}
// if this person is already hom var, he can't add another alternate allele
// so we can ignore that case
}
if ( greedyIndex == -1 )
throw new StingException("There is no best choice for a new alternate allele; how is this possible?");
if ( indexes[greedyIndex] == GenotypeType.HET.ordinal() )
indexes[greedyIndex] = GenotypeType.HOM.ordinal();
else
indexes[greedyIndex] = GenotypeType.HET.ordinal();
}
public double getLikelihoodsOfFrequency() {
double likelihoods = 0.0;
for (int i = 0; i < N; i++)
likelihoods += matrix[i][indexes[i]];
//verboseWriter.write(frequency + "\n");
//for (int i = 0; i < N; i++) {
// for (int j=0; j < 3; j++) {
// verboseWriter.write(String.valueOf(matrix[i][j]));
// verboseWriter.write(indexes[i] == j ? "* " : " ");
// }
// verboseWriter.write("\n");
//}
//verboseWriter.write(likelihoods + "\n\n");
return likelihoods;
}
}
}