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handle normal reads in validation sample in BasicSomaticValidator #5322

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merged 1 commit into from
Oct 18, 2018
Merged

handle normal reads in validation sample in BasicSomaticValidator #5322

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12 changes: 10 additions & 2 deletions ...nder/tools/walkers/validation/basicshortmutpileup/ValidateBasicSomaticShortMutations.java
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Original file line number Diff line number Diff line change
Expand Up @@ -54,8 +54,10 @@ public class ValidateBasicSomaticShortMutations extends VariantWalker {
public final static int DEFAULT_MIN_BQ_CUTOFF = 20;
public final static String CUTOFF_LONG_NAME = "min-base-quality-cutoff";
public final static String MIN_POWER_LONG_NAME = "min-power";
public final static String MAX_VALIDATION_NORMAL_COUNT_LONG_NAME = "max-validation-normal-count";

private static final double DEFAULT_MIN_POWER = 0.9;
private static final int DEFAULT_MAX_VALIDATION_NORMAL_COUNT = 1;

@Argument(fullName = SAMPLE_NAME_DISCOVERY_VCF_LONG_NAME,
doc = "sample name for discovery in VCF.")
Expand All @@ -81,6 +83,11 @@ public class ValidateBasicSomaticShortMutations extends VariantWalker {
optional = true)
protected double minPower = DEFAULT_MIN_POWER;

@Argument(doc = "Maximum read count in the validation normal for a variant to validate. More counts is considered an artifact.",
fullName = MAX_VALIDATION_NORMAL_COUNT_LONG_NAME,
optional = true)
protected int maxValidationNormalCount = DEFAULT_MAX_VALIDATION_NORMAL_COUNT;

@Argument(fullName = SAMPLE_NAME_VALIDATION_CASE,
doc = "validation case sample name (in the bam)")
protected String validationCaseName;
Expand Down Expand Up @@ -234,8 +241,9 @@ public void apply(VariantContext discoveryVariantContext, ReadsContext readsCont
results.add(basicValidationResult);
}

final boolean validated = basicValidationResult != null && basicValidationResult.isOutOfNoiseFloor();
final boolean powered = basicValidationResult != null && basicValidationResult.getPower() > minPower;
final boolean normalArtifact = basicValidationResult.getNumAltSupportingReadsInNormal() > maxValidationNormalCount;
final boolean validated = !normalArtifact && basicValidationResult != null && basicValidationResult.isOutOfNoiseFloor();
final boolean powered = normalArtifact || (basicValidationResult != null && basicValidationResult.getPower() > minPower);

if (discoveryVariantContext.isSNP()) {
if (validated) {
Expand Down