Account for overlapping reads in Theoretical Sensitivity model

src/main/java/picard/analysis/CollectWgsMetrics.java

@@ -139,6 +139,9 @@ public class CollectWgsMetrics extends CommandLineProgram {
  @Argument(doc="Allele fraction for which to calculate theoretical sensitivity.", optional = true)
  public List<Double> ALLELE_FRACTION = new ArrayList<>(Arrays.asList(0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5));
 
+ @Argument(doc="Maximum value allowed for base quality resulting from overlapping reads. Often this is governed by PCR error rate. (Phred scale)", optional = true)
+ public int MAX_OVERLAP_BASE_QUAL = 45;
+
  @Argument(doc = "If true, fast algorithm is used.")
  public boolean USE_FAST_ALGORITHM = false;
 
@@ -242,8 +245,11 @@ protected int doWork() {
  if (THEORETICAL_SENSITIVITY_OUTPUT != null) {
  // Write out theoretical sensitivity results.
  final MetricsFile<TheoreticalSensitivityMetrics, ?> theoreticalSensitivityMetrics = getMetricsFile();
- log.info("Calculating theoretical sentitivity at " + ALLELE_FRACTION.size() + " allele fractions.");
- List<TheoreticalSensitivityMetrics> tsm = TheoreticalSensitivity.calculateSensitivities(SAMPLE_SIZE, collector.getUnfilteredDepthHistogram(), collector.getUnfilteredBaseQHistogram(), ALLELE_FRACTION);
+ log.info("Calculating theoretical sensitivity at " + ALLELE_FRACTION.size() + " allele fractions.");
+
+ List<TheoreticalSensitivityMetrics> tsm = TheoreticalSensitivity.calculateSensitivities(SAMPLE_SIZE,
+ collector.getUnfilteredDepthHistogram(), collector.getUnfilteredBaseQHistogram(), ALLELE_FRACTION,
+ collector.getMetrics(dupeFilter, adapterFilter, mapqFilter, pairFilter).PCT_EXC_OVERLAP, MAX_OVERLAP_BASE_QUAL);
  theoreticalSensitivityMetrics.addAllMetrics(tsm);
  theoreticalSensitivityMetrics.write(THEORETICAL_SENSITIVITY_OUTPUT);
  }

src/main/java/picard/analysis/TheoreticalSensitivity.java

@@ -46,7 +46,6 @@ public class TheoreticalSensitivity {
  private static final Log log = Log.getInstance(TheoreticalSensitivity.class);
  private static final int SAMPLING_MAX = 600; //prevent 'infinite' loops
  private static final int MAX_CONSIDERED_DEPTH_HET_SENS = 1000; // No point in looking any deeper than this, otherwise GC overhead is too high. Only used for HET sensitivity.
- private static final int LARGE_NUMBER_OF_DRAWS = 10; // The number of draws at which we believe a Gaussian approximation to sum random variables.
  private static final double DEPTH_BIN_WIDTH = 0.01; // Minimal fraction of depth histogram to use when integrating theoretical sensitivity. This ensures we don't calculate theoretical sensitivity at every depth, which would be computationally expensive.
  private static final int RANDOM_SEED = 51;
 
@@ -241,9 +240,14 @@ public TheoreticalSensitivity() {
  * @param sampleSize sampleSize is the total number of simulations to run
  * @param alleleFraction the allele fraction to evaluate sensitivity at
  * @param randomSeed random number seed to use for random number generator
+ * @param overlapProbability Probability a position on a read overlaps with its mate
+ * @param maxOverlapBaseQuality Maximum base quality that can result from summing overlapping base qualities, often capped by PCR error rate
  * @return Theoretical sensitivity for the given arguments at a constant depth.
  */
- public static double sensitivityAtConstantDepth(final int depth, final Histogram<Integer> qualityHistogram, final double logOddsThreshold, final int sampleSize, final double alleleFraction, final long randomSeed) {
+ public static double sensitivityAtConstantDepth(final int depth, final Histogram<Integer> qualityHistogram,
+ final double logOddsThreshold, final int sampleSize,
+ final double alleleFraction, final long randomSeed,
+ final double overlapProbability, final int maxOverlapBaseQuality) {
  // If the depth is 0 at a particular locus, the sensitivity is trivially 0.0.
  if (depth == 0) {
  return 0.0;
@@ -264,37 +268,28 @@ public static double sensitivityAtConstantDepth(final int depth, final Histogram
  for (int sample = 0; sample < sampleSize; sample++) {
  final int altDepth = bd.sample();
 
- final int sumOfQualities;
- if (altDepth < LARGE_NUMBER_OF_DRAWS) {
- // If the number of alt reads is "small" we draw from the actual base quality distribution.
- sumOfQualities = IntStream.range(0, altDepth).map(n -> qualityRW.draw()).sum();
- } else {
- // If the number of alt reads is "large" we draw from a Gaussian approximation of the base
- // quality distribution to speed up the code.
- sumOfQualities = drawSumOfQScores(altDepth, averageQuality, standardDeviationQuality, randomNumberGenerator.nextGaussian());
+ int sumOfQualities;
+ // If the number of alt reads is "small" we draw from the actual base quality distribution.
+ sumOfQualities = 0;
+ for(int i = 0;i < altDepth;i++) {
+ if(rg.nextDouble() > overlapProbability) {
+ sumOfQualities += Math.min(qualityRW.draw(), maxOverlapBaseQuality);
+ } else {
+ // Simulate overlapping reads by sampling from the quality distribution twice.
+ // Since PCR errors affect overlapping reads, the total contribution to the sum
+ // of qualities cannot exceed the PCR error rate.
+ sumOfQualities += Math.min(qualityRW.draw() + qualityRW.draw(), maxOverlapBaseQuality);
+ }
  }
 
+
  if (isCalled(depth, altDepth, (double) sumOfQualities, alleleFraction, logOddsThreshold)) {
  calledVariants++;
  }
  }
  return (double) calledVariants / sampleSize;
  }
 
- /**
- * Simulates the sum of base qualities taken from reads that support the alternate allele by
- * taking advantage of the fact that the sum of draws from a distribution tends towards a
- * Gaussian per the Central Limit Theorem.
- * @param altDepth Number of draws to take from base quality distribution
- * @param averageQuality Average quality of alt bases
- * @param standardDeviationQuality Sample standard deviation of base quality scores
- * @param z number of standard deviation from the mean to take sum over
- * @return Simulated sum of base qualities the support the alternate allele
- */
- static int drawSumOfQScores(final int altDepth, final double averageQuality, final double standardDeviationQuality, final double z) {
- return (int) (altDepth * averageQuality + z * Math.sqrt(altDepth) * standardDeviationQuality);
- }
-
  /**
  * Calculates the theoretical sensitivity with a given Phred-scaled quality score distribution at a constant
  * depth.
@@ -305,8 +300,12 @@ static int drawSumOfQScores(final int altDepth, final double averageQuality, fin
  * @param alleleFraction the allele fraction to evaluate sensitivity at
  * @return Theoretical sensitivity for the given arguments at a constant depth.
  */
- private static double sensitivityAtConstantDepth(final int depth, final Histogram<Integer> qualityHistogram, final double logOddsThreshold, final int sampleSize, final double alleleFraction) {
- return sensitivityAtConstantDepth(depth, qualityHistogram, logOddsThreshold, sampleSize, alleleFraction, RANDOM_SEED);
+ private static double sensitivityAtConstantDepth(final int depth, final Histogram<Integer> qualityHistogram,
+ final double logOddsThreshold, final int sampleSize,
+ final double alleleFraction, final double overlapProbability,
+ final int pcrErrorRate) {
+ return sensitivityAtConstantDepth(depth, qualityHistogram, logOddsThreshold, sampleSize, alleleFraction,
+ RANDOM_SEED, overlapProbability, pcrErrorRate);
  }
 
  /**
@@ -317,10 +316,14 @@ private static double sensitivityAtConstantDepth(final int depth, final Histogra
  * @param sampleSize the total number of simulations to run
  * @param logOddsThreshold Log odds threshold necessary for variant to be called
  * @param alleleFraction the allele fraction to evaluate sensitivity at
+ * @param overlapProbability the probability two bases from the same fragment are overlapping
+ * @param pcrErrorRate Upper bound for the effective base quality two bases in an overlapping read
  * @return Theoretical sensitivity for the given arguments over a particular depth distribution.
  */
- public static double theoreticalSensitivity(final Histogram<Integer> depthHistogram, final Histogram<Integer> qualityHistogram,
- final int sampleSize, final double logOddsThreshold, final double alleleFraction) {
+ public static double theoreticalSensitivity(final Histogram<Integer> depthHistogram,
+ final Histogram<Integer> qualityHistogram, final int sampleSize,
+ final double logOddsThreshold, final double alleleFraction,
+ final double overlapProbability, final int pcrErrorRate) {
  if (alleleFraction > 1.0 || alleleFraction < 0.0) {
  throw new IllegalArgumentException("Allele fractions must be between 0 and 1.");
  }
@@ -346,7 +349,8 @@ public static double theoreticalSensitivity(final Histogram<Integer> depthHistog
  }
  // Calculate sensitivity for a particular depth, and use trapezoid rule to integrate sensitivity.
  final double left = right;
- right = sensitivityAtConstantDepth(currentDepth, qualityHistogram, logOddsThreshold, sampleSize, alleleFraction);
+ right = sensitivityAtConstantDepth(currentDepth, qualityHistogram, logOddsThreshold, sampleSize,
+ alleleFraction, overlapProbability, pcrErrorRate);
  sensitivity += deltaDepthProbability * (left + right) / 2.0;
  }
  return sensitivity;
@@ -386,7 +390,11 @@ static double[] trimDistribution(final double[] distribution) {
  * @param alleleFractions List of allele fractions to measure theoretical sensitivity over.
  */
  public static List<TheoreticalSensitivityMetrics> calculateSensitivities(final int simulationSize,
- final Histogram<Integer> depthHistogram, final Histogram<Integer> baseQHistogram, final List<Double> alleleFractions) {
+ final Histogram<Integer> depthHistogram,
+ final Histogram<Integer> baseQHistogram,
+ final List<Double> alleleFractions,
+ final double overlapProbability,
+ final int pcrErrorRate) {
 
  final List<TheoreticalSensitivityMetrics> metricsOverVariousAlleleFractions = new ArrayList<>();
  final double logOddsThreshold = 6.2; // This threshold is used because it is the value used for MuTect2.
@@ -396,7 +404,8 @@ public static List<TheoreticalSensitivityMetrics> calculateSensitivities(final i
  for (final double alleleFraction : alleleFractions) {
  final TheoreticalSensitivityMetrics theoreticalSensitivityMetrics = new TheoreticalSensitivityMetrics();
  theoreticalSensitivityMetrics.ALLELE_FRACTION = alleleFraction;
- theoreticalSensitivityMetrics.THEORETICAL_SENSITIVITY = TheoreticalSensitivity.theoreticalSensitivity(depthHistogram, baseQHistogram, simulationSize, logOddsThreshold, alleleFraction);
+ theoreticalSensitivityMetrics.THEORETICAL_SENSITIVITY = TheoreticalSensitivity.theoreticalSensitivity(
+ depthHistogram, baseQHistogram, simulationSize, logOddsThreshold, alleleFraction, overlapProbability, pcrErrorRate);
  theoreticalSensitivityMetrics.THEORETICAL_SENSITIVITY_Q = QualityUtil.getPhredScoreFromErrorProbability((1 - theoreticalSensitivityMetrics.THEORETICAL_SENSITIVITY));
  theoreticalSensitivityMetrics.SAMPLE_SIZE = simulationSize;
  theoreticalSensitivityMetrics.LOG_ODDS_THRESHOLD = logOddsThreshold;

src/main/java/picard/analysis/directed/CollectTargetedMetrics.java

@@ -105,6 +105,9 @@ protected abstract COLLECTOR makeCollector(final Set<MetricAccumulationLevel> ac
  @Argument(doc="Output for Theoretical Sensitivity metrics where the allele fractions are provided by the ALLELE_FRACTION argument.", optional = true)
  public File THEORETICAL_SENSITIVITY_OUTPUT;
 
+ @Argument(doc="Phred scaled PCR Error Rate for Theoretical Sensitivity model.", optional = true)
+ public int PCR_ERROR_RATE = 45;
+
  @Argument(doc="Allele fraction for which to calculate theoretical sensitivity.", optional = true)
  public List<Double> ALLELE_FRACTION = new ArrayList<>(Arrays.asList(0.001, 0.005, 0.01, 0.02, 0.05, 0.1, 0.2, 0.3, 0.5));
  /**
@@ -169,7 +172,11 @@ protected int doWork() {
  // Write out theoretical sensitivity results.
  final MetricsFile<TheoreticalSensitivityMetrics, ?> theoreticalSensitivityMetrics = getMetricsFile();
  log.info("Calculating theoretical sentitivity at " + ALLELE_FRACTION.size() + " allele fractions.");
- List<TheoreticalSensitivityMetrics> tsm = TheoreticalSensitivity.calculateSensitivities(SAMPLE_SIZE, collector.getDepthHistogram(), collector.getBaseQualityHistogram(), ALLELE_FRACTION);
+
+ final double overlapProbability = ((PanelMetricsBase) metrics.getMetrics().toArray()[0]).PCT_EXC_OVERLAP;
+
+ List<TheoreticalSensitivityMetrics> tsm = TheoreticalSensitivity.calculateSensitivities(SAMPLE_SIZE,
+ collector.getDepthHistogram(), collector.getBaseQualityHistogram(), ALLELE_FRACTION, overlapProbability, PCR_ERROR_RATE);
  theoreticalSensitivityMetrics.addAllMetrics(tsm);
  theoreticalSensitivityMetrics.write(THEORETICAL_SENSITIVITY_OUTPUT);
  }

src/main/java/picard/analysis/directed/TargetMetricsCollector.java

@@ -134,8 +134,6 @@ public abstract class TargetMetricsCollector<METRIC_TYPE extends MultilevelMetri
 
  private static final double LOG_ODDS_THRESHOLD = 3.0;
 
- private final File theoreticalSensitivityOutput = null;
-
  private final int minimumMappingQuality;
  private final int minimumBaseQuality;
  private final boolean clipOverlappingReads;

src/test/java/picard/IntelInflaterDeflaterLoadTest.java

@@ -26,7 +26,7 @@ public void testIntelDeflaterIsAvailable() {
  }
 
  private void checkIntelSupported(final String componentName) {
- if (!SystemUtils.IS_OS_LINUX && !SystemUtils.IS_OS_MAC) {
+ if ((!SystemUtils.IS_OS_LINUX && !SystemUtils.IS_OS_MAC)) {
  throw new SkipException(componentName + " is not available on this platform");
  }