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Simple extension to VariantEval: --includeFilteredRecords will now keep filtered VCF records so you can see what the entire call set looks like. Looking forward to VariantEval v2 from Kiran. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2506 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-01-06 12:59:09 +00:00
parent 8d13597a27
commit 21a50eedb5
1 changed files with 4 additions and 4 deletions
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8
java/src/org/broadinstitute/sting/playground/gatk/walkers/varianteval/VariantEvalWalker.java
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@ -48,8 +48,9 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
@Argument(fullName="supressDateInformation", doc="This flag indicates that we want to suppress the date information from the output, so that if can be diff'ed against previous evals.", required=false)
public boolean supressDateInformation = false;
//@Argument(fullName = "numPeopleInPool", shortName="PS", doc="If using a variant file from a pooled caller, this field provides the number of individuals in each pool", required=false)
//public int numPeopleInPool = -1;
@Argument(fullName="includeFilteredRecords", doc="If true, variation record with filter fields at are true will be included in the analysis", required=false)
public boolean includeFilteredRecords = false;
@Argument(fullName = "samplesFile", shortName="samples", doc="When running an analysis on one or more individuals with truth data, this field provides a filepath to the listing of which samples are used (and are used to name corresponding rods with -B)", required=false)
public String samplesFile = null;
@ -248,8 +249,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> {
if (eval.getNegLog10PError() * 10.0 < minConfidenceScore) eval = null;
if ( eval != null && (eval instanceof RodVCF) && ((RodVCF)eval).mCurrentRecord.isFiltered() ) {
//System.out.printf("Rejecting filtered record %s%n", eval);
eval = null;
if ( ! includeFilteredRecords ) eval = null; // we are not including filtered records, so set eval to null
}
// update stats about all of the SNPs