Class WgsMetrics

    • Field Summary

      Fields 
      Modifier and Type Field Description
      protected int coverageCap
      The maximum depth/coverage to consider.
      long GENOME_TERRITORY
      The number of non-N bases in the genome reference over which coverage will be evaluated.
      double HET_SNP_Q
      The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
      double HET_SNP_SENSITIVITY
      The theoretical HET SNP sensitivity.
      protected htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram
      Count of sites with a given depth of coverage.
      protected htsjdk.samtools.util.IntervalList intervals
      The intervals over which this metric was computed.
      double MAD_COVERAGE
      The median absolute deviation of coverage of the genome after all filters are applied.
      double MEAN_COVERAGE
      The mean coverage in bases of the genome territory, after all filters are applied.
      double MEDIAN_COVERAGE
      The median coverage in bases of the genome territory, after all filters are applied.
      double PCT_100X
      The fraction of bases that attained at least 100X sequence coverage in post-filtering bases.
      double PCT_10X
      The fraction of bases that attained at least 10X sequence coverage in post-filtering bases.
      double PCT_15X
      The fraction of bases that attained at least 15X sequence coverage in post-filtering bases.
      double PCT_1X
      The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.
      double PCT_20X
      The fraction of bases that attained at least 20X sequence coverage in post-filtering bases.
      double PCT_25X
      The fraction of bases that attained at least 25X sequence coverage in post-filtering bases.
      double PCT_30X
      The fraction of bases that attained at least 30X sequence coverage in post-filtering bases.
      double PCT_40X
      The fraction of bases that attained at least 40X sequence coverage in post-filtering bases.
      double PCT_50X
      The fraction of bases that attained at least 50X sequence coverage in post-filtering bases.
      double PCT_5X
      The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.
      double PCT_60X
      The fraction of bases that attained at least 60X sequence coverage in post-filtering bases.
      double PCT_70X
      The fraction of bases that attained at least 70X sequence coverage in post-filtering bases.
      double PCT_80X
      The fraction of bases that attained at least 80X sequence coverage in post-filtering bases.
      double PCT_90X
      The fraction of bases that attained at least 90X sequence coverage in post-filtering bases.
      double PCT_EXC_ADAPTER
      The fraction of aligned bases that were filtered out because they were in reads with mapping quality 0 and the looked like adapter reads.
      double PCT_EXC_BASEQ
      The fraction of aligned bases that were filtered out because they were of low base quality (lower than MIN_BASE_QUALITY).
      double PCT_EXC_CAPPED
      The fraction of aligned bases that were filtered out because they would have raised coverage above COVERAGE_CAP.
      double PCT_EXC_DUPE
      The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
      double PCT_EXC_MAPQ
      The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (lower than MIN_MAPPING_QUALITY).
      double PCT_EXC_OVERLAP
      The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
      double PCT_EXC_TOTAL
      The total fraction of aligned bases excluded due to all filters.
      double PCT_EXC_UNPAIRED
      The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.
      double SD_COVERAGE
      The standard deviation of coverage of the genome after all filters are applied.
      protected int theoreticalHetSensitivitySampleSize
      The sample size used for theoretical het sensitivity.
      protected htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram
      The count of bases observed with a given base quality.
      protected htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram
      Count of sites with a given depth of coverage.
    • Constructor Summary

      Constructors 
      Constructor Description
      WgsMetrics()
      Create an instance of this metric that is not mergeable.
      WgsMetrics​(htsjdk.samtools.util.IntervalList intervals, htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram, htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram, double pctExcludedByAdapter, double pctExcludedByMapq, double pctExcludedByDupes, double pctExcludedByPairing, double pctExcludedByBaseq, double pctExcludedByOverlap, double pctExcludedByCapping, double pctExcludeTotal, int coverageCap, htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram, int theoreticalHetSensitivitySampleSize)
      Create an instance of this metric that is mergeable.
    • Field Detail

      • intervals

        protected htsjdk.samtools.util.IntervalList intervals
        The intervals over which this metric was computed.
      • highQualityDepthHistogram

        protected final htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram
        Count of sites with a given depth of coverage. Excludes bases with quality below MINIMUM_BASE_QUALITY
      • unfilteredDepthHistogram

        protected final htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram
        Count of sites with a given depth of coverage. Includes all but quality 2 bases
      • unfilteredBaseQHistogram

        protected final htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram
        The count of bases observed with a given base quality.
      • coverageCap

        protected final int coverageCap
        The maximum depth/coverage to consider.
      • theoreticalHetSensitivitySampleSize

        protected final int theoreticalHetSensitivitySampleSize
        The sample size used for theoretical het sensitivity.
      • GENOME_TERRITORY

        public long GENOME_TERRITORY
        The number of non-N bases in the genome reference over which coverage will be evaluated.
      • MEAN_COVERAGE

        public double MEAN_COVERAGE
        The mean coverage in bases of the genome territory, after all filters are applied.
      • SD_COVERAGE

        public double SD_COVERAGE
        The standard deviation of coverage of the genome after all filters are applied.
      • MEDIAN_COVERAGE

        public double MEDIAN_COVERAGE
        The median coverage in bases of the genome territory, after all filters are applied.
      • MAD_COVERAGE

        public double MAD_COVERAGE
        The median absolute deviation of coverage of the genome after all filters are applied.
      • PCT_EXC_ADAPTER

        public double PCT_EXC_ADAPTER
        The fraction of aligned bases that were filtered out because they were in reads with mapping quality 0 and the looked like adapter reads.
      • PCT_EXC_MAPQ

        public double PCT_EXC_MAPQ
        The fraction of aligned bases that were filtered out because they were in reads with low mapping quality (lower than MIN_MAPPING_QUALITY).
      • PCT_EXC_DUPE

        public double PCT_EXC_DUPE
        The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
      • PCT_EXC_UNPAIRED

        public double PCT_EXC_UNPAIRED
        The fraction of aligned bases that were filtered out because they were in reads without a mapped mate pair.
      • PCT_EXC_BASEQ

        public double PCT_EXC_BASEQ
        The fraction of aligned bases that were filtered out because they were of low base quality (lower than MIN_BASE_QUALITY).
      • PCT_EXC_OVERLAP

        public double PCT_EXC_OVERLAP
        The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
      • PCT_EXC_CAPPED

        public double PCT_EXC_CAPPED
        The fraction of aligned bases that were filtered out because they would have raised coverage above COVERAGE_CAP.
      • PCT_EXC_TOTAL

        public double PCT_EXC_TOTAL
        The total fraction of aligned bases excluded due to all filters.
      • PCT_1X

        public double PCT_1X
        The fraction of bases that attained at least 1X sequence coverage in post-filtering bases.
      • PCT_5X

        public double PCT_5X
        The fraction of bases that attained at least 5X sequence coverage in post-filtering bases.
      • PCT_10X

        public double PCT_10X
        The fraction of bases that attained at least 10X sequence coverage in post-filtering bases.
      • PCT_15X

        public double PCT_15X
        The fraction of bases that attained at least 15X sequence coverage in post-filtering bases.
      • PCT_20X

        public double PCT_20X
        The fraction of bases that attained at least 20X sequence coverage in post-filtering bases.
      • PCT_25X

        public double PCT_25X
        The fraction of bases that attained at least 25X sequence coverage in post-filtering bases.
      • PCT_30X

        public double PCT_30X
        The fraction of bases that attained at least 30X sequence coverage in post-filtering bases.
      • PCT_40X

        public double PCT_40X
        The fraction of bases that attained at least 40X sequence coverage in post-filtering bases.
      • PCT_50X

        public double PCT_50X
        The fraction of bases that attained at least 50X sequence coverage in post-filtering bases.
      • PCT_60X

        public double PCT_60X
        The fraction of bases that attained at least 60X sequence coverage in post-filtering bases.
      • PCT_70X

        public double PCT_70X
        The fraction of bases that attained at least 70X sequence coverage in post-filtering bases.
      • PCT_80X

        public double PCT_80X
        The fraction of bases that attained at least 80X sequence coverage in post-filtering bases.
      • PCT_90X

        public double PCT_90X
        The fraction of bases that attained at least 90X sequence coverage in post-filtering bases.
      • PCT_100X

        public double PCT_100X
        The fraction of bases that attained at least 100X sequence coverage in post-filtering bases.
      • HET_SNP_SENSITIVITY

        public double HET_SNP_SENSITIVITY
        The theoretical HET SNP sensitivity.
      • HET_SNP_Q

        public double HET_SNP_Q
        The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
    • Constructor Detail

      • WgsMetrics

        public WgsMetrics()
        Create an instance of this metric that is not mergeable.
      • WgsMetrics

        public WgsMetrics​(htsjdk.samtools.util.IntervalList intervals,
                          htsjdk.samtools.util.Histogram<Integer> highQualityDepthHistogram,
                          htsjdk.samtools.util.Histogram<Integer> unfilteredDepthHistogram,
                          double pctExcludedByAdapter,
                          double pctExcludedByMapq,
                          double pctExcludedByDupes,
                          double pctExcludedByPairing,
                          double pctExcludedByBaseq,
                          double pctExcludedByOverlap,
                          double pctExcludedByCapping,
                          double pctExcludeTotal,
                          int coverageCap,
                          htsjdk.samtools.util.Histogram<Integer> unfilteredBaseQHistogram,
                          int theoreticalHetSensitivitySampleSize)
        Create an instance of this metric that is mergeable.
        Parameters:
        highQualityDepthHistogram - the count of genomic positions observed for each observed depth. Excludes bases with quality below MINIMUM_BASE_QUALITY.
        unfilteredDepthHistogram - the depth histogram that includes all but quality 2 bases.
        pctExcludedByAdapter - the fraction of aligned bases that were filtered out because they were in reads with 0 mapping quality that looked like adapter sequence.
        pctExcludedByMapq - the fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
        pctExcludedByDupes - the fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
        pctExcludedByPairing - the fraction of bases that were filtered out because they were in reads without a mapped mate pair.
        pctExcludedByBaseq - the fraction of aligned bases that were filtered out because they were of low base quality.
        pctExcludedByOverlap - the fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
        pctExcludedByCapping - the fraction of aligned bases that were filtered out because they would have raised coverage above the capped value.
        pctExcludeTotal - the fraction of bases excluded across all filters.
        coverageCap - Treat positions with coverage exceeding this value as if they had coverage at this value.
        unfilteredBaseQHistogram - the count of bases observed with a given quality. Includes all but quality 2 bases.
        theoreticalHetSensitivitySampleSize - the sample size used for theoretical het sensitivity sampling.
    • Method Detail

      • calculateDerivedFields

        public void calculateDerivedFields()
        Description copied from class: MergeableMetricBase
        Placeholder method that will calculate the derived fields from the other ones. Classes that are derived from non-trivial derived classes should consider calling super.calculateDerivedFields() as well. Fields whose value will change due to this method should be annotated with NoMergingKeepsValue.
        Overrides:
        calculateDerivedFields in class MergeableMetricBase