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Removing requirement of providing known track in VQSR for the non-humans. Updating placement of legend on tranche plot. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5773 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2011-05-05 20:24:06 +00:00
parent 04f156d86b
commit b94d8dae17
2 changed files with 2 additions and 5 deletions
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2
R/plot_Tranches.R
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@ -66,7 +66,7 @@ barplot(d/1000,horiz=TRUE,col=cols,space=0.2,xlab="Number of Novel Variants (100
#abline(v= d[2,dim(d)[2]], lty=2)
#abline(v= d[1,3], lty=2)
if ( ! suppressLegend )
legend(5, length(data2$targetTruthSensitivity)-1.25, c('Cumulative TPs','Tranch-specific TPs', 'Tranch-specific FPs', 'Cumulative FPs' ), fill=cols, density=density, bg='white', cex=1.25)
legend(3, length(data2$targetTruthSensitivity)/3 +1, c('Cumulative TPs','Tranch-specific TPs', 'Tranch-specific FPs', 'Cumulative FPs' ), fill=cols, density=density, bg='white', cex=1.25)
mtext("Ti/Tv",2,line=2.25,at=length(data2$targetTruthSensitivity)*1.2,las=1, cex=1)
mtext("truth",2,line=0,at=length(data2$targetTruthSensitivity)*1.2,las=1, cex=1)

5
java/src/org/broadinstitute/sting/gatk/walkers/variantrecalibration/VariantRecalibrator.java
View File

@ -135,9 +135,6 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
if( !dataManager.checkHasTruthSet() ) {
throw new UserException.CommandLineException( "No truth set found! Please provide sets of known polymorphic loci marked with the truth=true ROD binding tag. For example, -B:hapmap,VCF,known=false,training=true,truth=true,prior=12.0 hapmapFile.vcf" );
}
if( !dataManager.checkHasKnownSet() ) {
throw new UserException.CommandLineException( "No known set found! Please provide sets of known polymorphic loci marked with the known=true ROD binding tag. For example, -B:dbsnp,VCF,known=true,training=false,truth=false,prior=8.0 dbsnpFile.vcf" );
}
if( inputNames.size() == 0 ) {
throw new UserException.BadInput( "No input variant tracks found. Input variant binding names must begin with 'input'." );
@ -326,7 +323,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
for( final VariantDatum datum : randomData ) {
stream.print(String.format("%.3f, %.3f, %.3f, %d, %d,", datum.annotations[iii], datum.annotations[jjj], (datum.lod < lodCutoff ? -1.0 : 1.0), datum.usedForTraining, (datum.isKnown ? 1 : -1)));
}
stream.println("NA,NA,NA,NA,NA)");
stream.println("NA,NA,NA,NA,1)");
stream.println("d <- matrix(data,ncol=5,byrow=T)");
final String surfaceFrame = "sf." + USE_ANNOTATIONS[iii] + "." + USE_ANNOTATIONS[jjj];