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- add name to vcf od field 

- don't do HW calculation if everything is a no-call


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2936 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2010-03-05 01:43:01 +00:00
parent 7104a3a96c
commit 9f7ebe1e1c
2 changed files with 9 additions and 4 deletions
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2
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
View File

@ -249,6 +249,8 @@ public class VariantContextUtils {
public static double computeHardyWeinbergPvalue(VariantContext vc) { public static double computeHardyWeinbergPvalue(VariantContext vc) {
if ( vc.getChromosomeCount() == 0 )
return 0.0;
return HardyWeinbergCalculation.hwCalculate(vc.getHomRefCount(), vc.getHetCount(), vc.getHomVarCount()); return HardyWeinbergCalculation.hwCalculate(vc.getHomRefCount(), vc.getHetCount(), vc.getHomVarCount());
} }

11
java/src/org/broadinstitute/sting/playground/gatk/walkers/variantstovcf/PlinkToVCF.java
View File

@ -158,12 +158,12 @@ public class PlinkToVCF extends RodWalker<VCFRecord,Integer> {
double hetProp = (double)vContext.getHetCount() / (double)vContext.getNSamples(); double hetProp = (double)vContext.getHetCount() / (double)vContext.getNSamples();
double homVarProp = (double)vContext.getHomVarCount() / (double)vContext.getNSamples(); double homVarProp = (double)vContext.getHomVarCount() / (double)vContext.getNSamples();
if ( hwScore > maxHardy ) { if ( noCallProp > maxNoCall ) {
record.setFilterString("HardyWeinbergViolation");
numHWViolations++;
} else if ( noCallProp > maxNoCall ) {
record.setFilterString("HighNoCallRate"); record.setFilterString("HighNoCallRate");
numNoCallViolations++; numNoCallViolations++;
} else if ( hwScore > maxHardy ) {
record.setFilterString("HardyWeinbergViolation");
numHWViolations++;
} else if ( homVarProp > maxHomNonref) { } else if ( homVarProp > maxHomNonref) {
record.setFilterString("TooManyHomVars"); record.setFilterString("TooManyHomVars");
numHomVarViolations++; numHomVarViolations++;
@ -183,6 +183,9 @@ public class PlinkToVCF extends RodWalker<VCFRecord,Integer> {
infoMap.put(VCFRecord.ALLELE_NUMBER_KEY, String.format("%d", vContext.getChromosomeCount())); infoMap.put(VCFRecord.ALLELE_NUMBER_KEY, String.format("%d", vContext.getChromosomeCount()));
record.addInfoFields(infoMap); record.addInfoFields(infoMap);
// add the id
record.setID(plinkRod.getVariantName());
return record; return record;
} }