zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Cleaned up this annotation. 

Still experimental.  As of now, it's not useful.  More analysis is needed to determine how to handle cases where UG is unsure whether a sample is het or hom.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2442 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks 2009-12-24 03:06:46 +00:00
parent 6df40876a3
commit aaf674d9db
1 changed files with 9 additions and 1 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

10
java/src/org/broadinstitute/sting/gatk/walkers/annotator/HardyWeinberg.java
View File

@ -30,6 +30,11 @@ public class HardyWeinberg implements VariantAnnotation {
for ( Genotype genotype : genotypes ) { for ( Genotype genotype : genotypes ) {
if ( genotype.isNoCall() ) if ( genotype.isNoCall() )
continue; continue;
// TODO - fix me:
// Right now we just ignore genotypes that are not confident, but this throws off
// our HW ratios. More analysis is needed to determine the right thing to do when
// the genotyper cannot decide whether a given sample is het or hom var.
if ( genotype.getNegLog10PError() < MIN_NEG_LOG10_PERROR ) if ( genotype.getNegLog10PError() < MIN_NEG_LOG10_PERROR )
continue; continue;
@ -41,8 +46,11 @@ public class HardyWeinberg implements VariantAnnotation {
homCount++; homCount++;
} }
if ( refCount + hetCount + homCount == 0)
return null;
double pvalue = HardyWeinbergCalculation.hwCalculate(refCount, hetCount, homCount); double pvalue = HardyWeinbergCalculation.hwCalculate(refCount, hetCount, homCount);
System.out.println(refCount + " " + hetCount + " " + homCount + " " + pvalue); //System.out.println(refCount + " " + hetCount + " " + homCount + " " + pvalue);
return String.format("%.1f", QualityUtils.phredScaleErrorRate(pvalue)); return String.format("%.1f", QualityUtils.phredScaleErrorRate(pvalue));
} }