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Adding a mode to VariantFiltration to invalidate previously-applied filters to allow complete re-filtering of a VCF. 

T2D VQSR: re-calling now done with appropriate quality settings and using BAQ.
This commit is contained in:
Christopher Hartl 2012-01-19 10:54:48 -05:00
parent ecdd07b748
commit 7f3ad25b01
1 changed files with 9 additions and 0 deletions
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9
public/java/src/org/broadinstitute/sting/gatk/walkers/filters/VariantFiltrationWalker.java
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@ -139,6 +139,12 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
@Argument(fullName="missingValuesInExpressionsShouldEvaluateAsFailing", doc="When evaluating the JEXL expressions, missing values should be considered failing the expression", required=false)
protected Boolean FAIL_MISSING_VALUES = false;
/**
* Invalidate previous filters applied to the VariantContext, applying only the filters here
*/
@Argument(fullName="invalidatePreviousFilters",doc="Remove previous filters applied to the VCF",required=false)
boolean invalidatePrevious = false;
// JEXL expressions for the filters
List<VariantContextUtils.JexlVCMatchExp> filterExps;
List<VariantContextUtils.JexlVCMatchExp> genotypeFilterExps;
@ -215,6 +221,9 @@ public class VariantFiltrationWalker extends RodWalker<Integer, Integer> {
for ( VariantContext vc : VCs ) {
if ( invalidatePrevious ) {
vc = (new VariantContextBuilder(vc)).filters(new HashSet<String>()).make();
}
// filter based on previous mask position
if ( previousMaskPosition != null && // we saw a previous mask site
previousMaskPosition.getContig().equals(vc.getChr()) && // it's on the same contig