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CountFalsePositives now requires an intervals file #6120

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Merged
merged 2 commits into from
Sep 9, 2019
Merged

CountFalsePositives now requires an intervals file #6120

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CountFalsePositives now requires an intervals file
takutosato Aug 26, 2019
7f9c2a5
megan
takutosato Aug 26, 2019
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13 changes: 8 additions & 5 deletions ...main/java/org/broadinstitute/hellbender/tools/walkers/validation/CountFalsePositives.java
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Original file line number Diff line number Diff line change
Expand Up @@ -31,6 +31,7 @@
* gatk --java-options "-Xmx4g" CountFalsePositives \
* -V filtered.vcf.gz \
* -R ref_fasta.fa \
* -L target_panel.interval_list \
* -O false-positives.txt
* </pre>
*
Expand All @@ -49,16 +50,18 @@ public class CountFalsePositives extends VariantWalker {
static final String USAGE_ONE_LINE_SUMMARY = "Count PASS variants";
static final String USAGE_SUMMARY = "Count PASS (false positive) variants in a vcf file for Mutect2 NA12878 normal-normal evaluation";

@Argument(
fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME,
shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME,
doc = "Output file"
)
@Argument(fullName = StandardArgumentDefinitions.OUTPUT_LONG_NAME, shortName = StandardArgumentDefinitions.OUTPUT_SHORT_NAME, doc = "Output file")
private File outputFile = null;

long indelFalsePositiveCount = 0;
long snpFalsePositiveCount = 0;
String id;

@Override
public boolean requiresIntervals() {
return true;
}

// TODO: eventually use tumor and normal sample names instead of the file name. To do so we must extract them from the vcf, which I don't know how.
@Override
public void onTraversalStart() {
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