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Fix no-normal bug; add HapMap sensitivity benchmarking

This commit is contained in:
Laura Gauthier 2015-09-01 08:09:38 -04:00
parent 0c3c775566
commit f9e9d2e273
1 changed files with 4 additions and 3 deletions
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7
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/cancer/m2/SomaticGenotypingEngine.java
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@ -261,7 +261,8 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
// remove the effect of cosmic from dbSNP // remove the effect of cosmic from dbSNP
boolean germlineAtRisk = (!dbsnpVC.isEmpty() && cosmicVC.isEmpty()); boolean germlineAtRisk = (!dbsnpVC.isEmpty() && cosmicVC.isEmpty());
NORMAL_LOD_THRESHOLD = (germlineAtRisk)?MTAC.NORMAL_DBSNP_LOD_THRESHOLD:MTAC.NORMAL_LOD_THRESHOLD; INIT_NORMAL_LOD_THRESHOLD = MTAC.INITIAL_NORMAL_LOD_THRESHOLD; //only set this if this job has a normal
NORMAL_LOD_THRESHOLD = (germlineAtRisk)?MTAC.NORMAL_DBSNP_LOD_THRESHOLD:MTAC.NORMAL_LOD_THRESHOLD;
for (int altInd = 0; altInd < numAlts; altInd++) for (int altInd = 0; altInd < numAlts; altInd++)
normalLods[altInd] = normalGLs[REF_INDEX] - normalGLs[altInd+1]; normalLods[altInd] = normalGLs[REF_INDEX] - normalGLs[altInd+1];
} }
@ -270,7 +271,7 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
int numPassingAlts = 0; int numPassingAlts = 0;
int lodInd = 0; int lodInd = 0;
for (int altInd = 0; altInd < numAlts; altInd++) { for (int altInd = 0; altInd < numAlts; altInd++) {
if (tumorLods[altInd] >= MTAC.INITIAL_TUMOR_LOD_THRESHOLD && normalLods[altInd] >= MTAC.INITIAL_NORMAL_LOD_THRESHOLD) { if (tumorLods[altInd] >= MTAC.INITIAL_TUMOR_LOD_THRESHOLD && normalLods[altInd] >= INIT_NORMAL_LOD_THRESHOLD) {
numPassingAlts++; numPassingAlts++;
lodInd = altInd; lodInd = altInd;
} }
@ -280,7 +281,7 @@ public class SomaticGenotypingEngine extends HaplotypeCallerGenotypingEngine {
final double normalLod = normalLods[lodInd]; final double normalLod = normalLods[lodInd];
VariantContext call = null; VariantContext call = null;
if (tumorLod >= MTAC.INITIAL_TUMOR_LOD_THRESHOLD && normalLod >= MTAC.INITIAL_NORMAL_LOD_THRESHOLD) { if (tumorLod >= MTAC.INITIAL_TUMOR_LOD_THRESHOLD && normalLod >= INIT_NORMAL_LOD_THRESHOLD) {
VariantContextBuilder callVcb = new VariantContextBuilder(mergedVC); VariantContextBuilder callVcb = new VariantContextBuilder(mergedVC);
if (normalLod < NORMAL_LOD_THRESHOLD) { if (normalLod < NORMAL_LOD_THRESHOLD) {