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Useful debugging argument added to VariantRecalibrator to only use sites whose qual field is above --qual 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4406 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
rpoplin 2010-10-01 21:08:55 +00:00
parent 575c38fc04
commit 2f7892601c
2 changed files with 66 additions and 61 deletions
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2
java/src/org/broadinstitute/sting/gatk/contexts/variantcontext/VariantContextUtils.java
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@ -312,7 +312,7 @@ public class VariantContextUtils {
String rsID = null; String rsID = null;
int depth = 0; int depth = 0;
// counting the number of filtered and varint VCs // counting the number of filtered and variant VCs
int nFiltered = 0, nVariant = 0; int nFiltered = 0, nVariant = 0;
Allele refAllele = determineReferenceAllele(VCs); Allele refAllele = determineReferenceAllele(VCs);

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

@ -116,6 +116,9 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
@Hidden @Hidden
@Argument(fullName = "NoByHapMapValidationStatus", shortName = "NoByHapMapValidationStatus", doc = "Don't consider sites in dbsnp rod tagged as by-hapmap validation status as real HapMap sites. FOR DEBUGGING PURPOSES ONLY.", required=false) @Argument(fullName = "NoByHapMapValidationStatus", shortName = "NoByHapMapValidationStatus", doc = "Don't consider sites in dbsnp rod tagged as by-hapmap validation status as real HapMap sites. FOR DEBUGGING PURPOSES ONLY.", required=false)
private Boolean NO_BY_HAPMAP_VALIDATION_STATUS = false; private Boolean NO_BY_HAPMAP_VALIDATION_STATUS = false;
@Hidden
@Argument(fullName = "qual", shortName = "qual", doc = "Don't use sites below the qual threshold. FOR DEBUGGING PURPOSES ONLY.", required=false)
private double QUAL_THRESHOLD = 0.0;
///////////////////////////// /////////////////////////////
// Private Member Variables // Private Member Variables
@ -217,6 +220,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
for( final VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), false, false) ) { for( final VariantContext vc : tracker.getVariantContexts(ref, inputNames, null, context.getLocation(), false, false) ) {
if( vc != null && vc.isSNP() ) { if( vc != null && vc.isSNP() ) {
if( !vc.isFiltered() || IGNORE_ALL_INPUT_FILTERS || (ignoreInputFilterSet != null && ignoreInputFilterSet.containsAll(vc.getFilters())) ) { if( !vc.isFiltered() || IGNORE_ALL_INPUT_FILTERS || (ignoreInputFilterSet != null && ignoreInputFilterSet.containsAll(vc.getFilters())) ) {
if( vc.getPhredScaledQual() >= QUAL_THRESHOLD ) {
final VariantDatum variantDatum = new VariantDatum(); final VariantDatum variantDatum = new VariantDatum();
variantDatum.isTransition = VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0; variantDatum.isTransition = VariantContextUtils.getSNPSubstitutionType(vc).compareTo(BaseUtils.BaseSubstitutionType.TRANSITION) == 0;
@ -287,6 +291,7 @@ public class VariantRecalibrator extends RodWalker<ExpandingArrayList<VariantDat
VariantContext newVC = VariantContext.modifyPErrorFiltersAndAttributes(vc, variantDatum.qual / 10.0, new HashSet<String>(), attrs); VariantContext newVC = VariantContext.modifyPErrorFiltersAndAttributes(vc, variantDatum.qual / 10.0, new HashSet<String>(), attrs);
vcfWriter.add( newVC, ref.getBase() ); vcfWriter.add( newVC, ref.getBase() );
}
} else { // not a SNP or is filtered so just dump it out to the VCF file } else { // not a SNP or is filtered so just dump it out to the VCF file
vcfWriter.add( vc, ref.getBase() ); vcfWriter.add( vc, ref.getBase() );