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Updating MD5s for confidence ref site estimation in IndependentAllelesDiploidExactAFCalc 

-- Included logic to only add priors for alleles with sufficient evidence to be called polymorphic.  If no alleles are poly make sure to add priors of first allele
This commit is contained in:
Mark DePristo 2012-10-23 06:47:53 -04:00
parent 15b28e61cd
commit f838815343
2 changed files with 10 additions and 2 deletions
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8
public/java/src/org/broadinstitute/sting/gatk/walkers/genotyper/afcalc/IndependentAllelesDiploidExactAFCalc.java
View File

@ -329,6 +329,7 @@ import java.util.*;
double log10PosteriorOfACEq0Sum = 0.0;
double log10PosteriorOfACGt0Sum = 0.0;
boolean anyPoly = false;
for ( final AFCalcResult sortedResultWithThetaNPriors : sortedResultsWithThetaNPriors ) {
final Allele altAllele = sortedResultWithThetaNPriors.getAllelesUsedInGenotyping().get(1);
final int altI = vc.getAlleles().indexOf(altAllele) - 1;
@ -338,6 +339,7 @@ import java.util.*;
// the AF > 0 case requires us to store the normalized likelihood for later summation
if ( sortedResultWithThetaNPriors.getLog10PosteriorOfAFGT0() > MIN_LOG10_CONFIDENCE_TO_INCLUDE_ALLELE_IN_POSTERIOR ) {
anyPoly = true;
log10PosteriorOfACEq0Sum += sortedResultWithThetaNPriors.getLog10PosteriorOfAFEq0();
log10PriorsOfAC[0] += sortedResultWithThetaNPriors.getLog10PriorOfAFEq0();
log10PriorsOfAC[1] += sortedResultWithThetaNPriors.getLog10PriorOfAFGT0();
@ -352,6 +354,12 @@ import java.util.*;
nEvaluations += sortedResultWithThetaNPriors.nEvaluations;
}
// If no alleles were polymorphic, make sure we have the proper priors (the defaults) for likelihood calculation
if ( ! anyPoly ) {
log10PriorsOfAC[0] = sortedResultsWithThetaNPriors.get(0).getLog10PriorOfAFEq0();
log10PriorsOfAC[1] = sortedResultsWithThetaNPriors.get(0).getLog10PriorOfAFGT0();
}
// In principle, if B_p = x and C_p = y are the probabilities of being poly for alleles B and C,
// the probability of being poly is (1 - B_p) * (1 - C_p) = (1 - x) * (1 - y). We want to estimate confidently
// log10((1 - x) * (1 - y)) which is log10(1 - x) + log10(1 - y). This sum is log10PosteriorOfACEq0

4
public/java/test/org/broadinstitute/sting/gatk/walkers/genotyper/UnifiedGenotyperIntegrationTest.java
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@ -192,12 +192,12 @@ public class UnifiedGenotyperIntegrationTest extends WalkerTest {
@Test
public void testOutputParameterAllConfident() {
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "8800c58715c2bb434b69e1873cb77de6");
testOutputParameters("--output_mode EMIT_ALL_CONFIDENT_SITES", "f9ea04d96eeef29e71d37e60518c2579");
}
@Test
public void testOutputParameterAllSites() {
testOutputParameters("--output_mode EMIT_ALL_SITES", "639df9f4c029792ac2e46069efc82b20");
testOutputParameters("--output_mode EMIT_ALL_SITES", "41c046d38ea328421df924e37e017645");
}
private void testOutputParameters(final String args, final String md5) {