Class TargetMetrics


  • public class TargetMetrics
    extends MultilevelMetrics
    TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA). TargetMetrics at the moment are the metrics that are shared by both HybridSelection and TargetedPcrMetrics.
    • Field Summary

      Fields 
      Modifier and Type Field Description
      double AT_DROPOUT
      A measure of how undercovered <= 50% GC regions are relative to the mean.
      double FOLD_80_BASE_PENALTY
      The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.
      double FOLD_ENRICHMENT
      The fold by which the probed region has been amplified above genomic background, (ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES))/(PROBE_TERRITORY/GENOME_SIZE)
      double GC_DROPOUT
      A measure of how undercovered >= 50% GC regions are relative to the mean.
      long GENOME_SIZE
      The number of bases in the reference genome used for alignment.
      double HET_SNP_Q
      The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
      double HET_SNP_SENSITIVITY
      The theoretical HET SNP sensitivity.
      long MAX_TARGET_COVERAGE
      The maximum coverage of reads that mapped to target regions of an experiment.
      double MEAN_PROBE_COVERAGE
      The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.
      double MEAN_TARGET_COVERAGE
      The mean coverage of targets.
      double MEDIAN_TARGET_COVERAGE
      The median coverage of targets.
      long NEAR_PROBE_BASES
      The number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a baited region.
      long OFF_PROBE_BASES
      The number of PF aligned bases that mapped to neither on or near a probe.
      long ON_PROBE_BASES
      The number of PF aligned probed bases that mapped to a baited region of the genome.
      double ON_PROBE_VS_SELECTED
      The fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES).
      long ON_TARGET_BASES
      The number of PF aligned bases that mapped to a targeted region of the genome.
      long ON_TARGET_FROM_PAIR_BASES
      The number of PF aligned bases that are mapped in pair to a targeted region of the genome.
      double PCT_EXC_BASEQ
      The fraction of aligned bases that were filtered out because they were of low base quality.
      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.
      double PCT_EXC_OFF_TARGET
      The fraction of aligned bases that were filtered out because they did not align over a target base.
      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_OFF_PROBE
      The fraction of aligned PF bases that mapped neither on or near a probe, OFF_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
      double PCT_PF_READS
      The fraction of reads passing filter, PF_READS/TOTAL_READS.
      double PCT_PF_UQ_READS
      The fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS.
      double PCT_PF_UQ_READS_ALIGNED
      The fraction of unique reads passing filter that align to the reference, PF_UQ_READS_ALIGNED/PF_UNIQUE_READS.
      double PCT_SELECTED_BASES
      The fraction of bases that map on or near a probe (ON_PROBE_BASES + NEAR_PROBE_BASES)/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
      double PCT_TARGET_BASES_100X
      The fraction of all target bases achieving 100X or greater coverage.
      double PCT_TARGET_BASES_10X
      The fraction of all target bases achieving 10X or greater coverage.
      double PCT_TARGET_BASES_1X
      The fraction of all target bases achieving 1X or greater coverage.
      double PCT_TARGET_BASES_20X
      The fraction of all target bases achieving 20X or greater coverage.
      double PCT_TARGET_BASES_2X
      The fraction of all target bases achieving 2X or greater coverage.
      double PCT_TARGET_BASES_30X
      The fraction of all target bases achieving 30X or greater coverage.
      double PCT_TARGET_BASES_40X
      The fraction of all target bases achieving 40X or greater coverage.
      double PCT_TARGET_BASES_50X
      The fraction of all target bases achieving 50X or greater coverage.
      long PF_BASES
      The number of bases in the PF_READS of a SAM or BAM file
      long PF_BASES_ALIGNED
      The number of PF_BASES that are aligned with mapping score > 0 to the reference genome.
      long PF_READS
      The number of passing filter reads (PF).
      long PF_SELECTED_PAIRS
      Tracks the number of read pairs that we see that are PF (used to calculate library size)
      long PF_SELECTED_UNIQUE_PAIRS
      Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)
      long PF_UNIQUE_READS
      The number of PF_READS that are not marked as duplicates.
      long PF_UQ_BASES_ALIGNED
      The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
      long PF_UQ_READS_ALIGNED
      The number of PF_UNIQUE_READS that are aligned with mapping score > 0 to the reference genome.
      String PROBE_SET
      The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run
      long PROBE_TERRITORY
      The number of unique bases covered by the intervals of all probes in the probe set
      long TARGET_TERRITORY
      The number of unique bases covered by the intervals of all targets that should be covered
      long TOTAL_READS
      The total number of reads in the SAM or BAM file examined.
      double ZERO_CVG_TARGETS_PCT
      The fraction of targets that did not reach coverage=1 over any base.
    • Constructor Summary

      Constructors 
      Constructor Description
      TargetMetrics()  
    • Field Detail

      • PROBE_SET

        public String PROBE_SET
        The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run
      • PROBE_TERRITORY

        public long PROBE_TERRITORY
        The number of unique bases covered by the intervals of all probes in the probe set
      • TARGET_TERRITORY

        public long TARGET_TERRITORY
        The number of unique bases covered by the intervals of all targets that should be covered
      • GENOME_SIZE

        public long GENOME_SIZE
        The number of bases in the reference genome used for alignment.
      • TOTAL_READS

        public long TOTAL_READS
        The total number of reads in the SAM or BAM file examined.
      • PF_READS

        public long PF_READS
        The number of passing filter reads (PF).
      • PF_BASES

        public long PF_BASES
        The number of bases in the PF_READS of a SAM or BAM file
      • PF_UNIQUE_READS

        public long PF_UNIQUE_READS
        The number of PF_READS that are not marked as duplicates.
      • PF_SELECTED_PAIRS

        public long PF_SELECTED_PAIRS
        Tracks the number of read pairs that we see that are PF (used to calculate library size)
      • PF_SELECTED_UNIQUE_PAIRS

        public long PF_SELECTED_UNIQUE_PAIRS
        Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)
      • PF_UQ_READS_ALIGNED

        public long PF_UQ_READS_ALIGNED
        The number of PF_UNIQUE_READS that are aligned with mapping score > 0 to the reference genome.
      • PF_BASES_ALIGNED

        public long PF_BASES_ALIGNED
        The number of PF_BASES that are aligned with mapping score > 0 to the reference genome.
      • PF_UQ_BASES_ALIGNED

        public long PF_UQ_BASES_ALIGNED
        The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
      • ON_PROBE_BASES

        public long ON_PROBE_BASES
        The number of PF aligned probed bases that mapped to a baited region of the genome.
      • NEAR_PROBE_BASES

        public long NEAR_PROBE_BASES
        The number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a baited region.
      • OFF_PROBE_BASES

        public long OFF_PROBE_BASES
        The number of PF aligned bases that mapped to neither on or near a probe.
      • ON_TARGET_BASES

        public long ON_TARGET_BASES
        The number of PF aligned bases that mapped to a targeted region of the genome.
      • ON_TARGET_FROM_PAIR_BASES

        public long ON_TARGET_FROM_PAIR_BASES
        The number of PF aligned bases that are mapped in pair to a targeted region of the genome.
      • PCT_PF_READS

        public double PCT_PF_READS
        The fraction of reads passing filter, PF_READS/TOTAL_READS.
      • PCT_PF_UQ_READS

        public double PCT_PF_UQ_READS
        The fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS.
      • PCT_PF_UQ_READS_ALIGNED

        public double PCT_PF_UQ_READS_ALIGNED
        The fraction of unique reads passing filter that align to the reference, PF_UQ_READS_ALIGNED/PF_UNIQUE_READS.
      • PCT_SELECTED_BASES

        public double PCT_SELECTED_BASES
        The fraction of bases that map on or near a probe (ON_PROBE_BASES + NEAR_PROBE_BASES)/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
      • PCT_OFF_PROBE

        public double PCT_OFF_PROBE
        The fraction of aligned PF bases that mapped neither on or near a probe, OFF_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
      • ON_PROBE_VS_SELECTED

        public double ON_PROBE_VS_SELECTED
        The fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES).
      • MEAN_PROBE_COVERAGE

        public double MEAN_PROBE_COVERAGE
        The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.
      • FOLD_ENRICHMENT

        public double FOLD_ENRICHMENT
        The fold by which the probed region has been amplified above genomic background, (ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES))/(PROBE_TERRITORY/GENOME_SIZE)
      • MEAN_TARGET_COVERAGE

        public double MEAN_TARGET_COVERAGE
        The mean coverage of targets.
      • MEDIAN_TARGET_COVERAGE

        public double MEDIAN_TARGET_COVERAGE
        The median coverage of targets.
      • MAX_TARGET_COVERAGE

        public long MAX_TARGET_COVERAGE
        The maximum coverage of reads that mapped to target regions of an experiment.
      • ZERO_CVG_TARGETS_PCT

        public double ZERO_CVG_TARGETS_PCT
        The fraction of targets that did not reach coverage=1 over any base.
      • 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_MAPQ

        public double PCT_EXC_MAPQ
        The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
      • PCT_EXC_BASEQ

        public double PCT_EXC_BASEQ
        The fraction of aligned bases that were filtered out because they were of low 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_OFF_TARGET

        public double PCT_EXC_OFF_TARGET
        The fraction of aligned bases that were filtered out because they did not align over a target base.
      • FOLD_80_BASE_PENALTY

        public double FOLD_80_BASE_PENALTY
        The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.
      • PCT_TARGET_BASES_1X

        public double PCT_TARGET_BASES_1X
        The fraction of all target bases achieving 1X or greater coverage.
      • PCT_TARGET_BASES_2X

        public double PCT_TARGET_BASES_2X
        The fraction of all target bases achieving 2X or greater coverage.
      • PCT_TARGET_BASES_10X

        public double PCT_TARGET_BASES_10X
        The fraction of all target bases achieving 10X or greater coverage.
      • PCT_TARGET_BASES_20X

        public double PCT_TARGET_BASES_20X
        The fraction of all target bases achieving 20X or greater coverage.
      • PCT_TARGET_BASES_30X

        public double PCT_TARGET_BASES_30X
        The fraction of all target bases achieving 30X or greater coverage.
      • PCT_TARGET_BASES_40X

        public double PCT_TARGET_BASES_40X
        The fraction of all target bases achieving 40X or greater coverage.
      • PCT_TARGET_BASES_50X

        public double PCT_TARGET_BASES_50X
        The fraction of all target bases achieving 50X or greater coverage.
      • PCT_TARGET_BASES_100X

        public double PCT_TARGET_BASES_100X
        The fraction of all target bases achieving 100X or greater coverage.
      • AT_DROPOUT

        public double AT_DROPOUT
        A measure of how undercovered <= 50% GC regions are relative to the mean. For each GC bin [0..50] we calculate a = % of target territory, and b = % of aligned reads aligned to these targets. AT DROPOUT is then abs(sum(a-b when a-b < 0)). E.g. if the value is 5% this implies that 5% of total reads that should have mapped to GC<=50% regions mapped elsewhere.
      • GC_DROPOUT

        public double GC_DROPOUT
        A measure of how undercovered >= 50% GC regions are relative to the mean. For each GC bin [50..100] we calculate a = % of target territory, and b = % of aligned reads aligned to these targets. GC DROPOUT is then abs(sum(a-b when a-b < 0)). E.g. if the value is 5% this implies that 5% of total reads that should have mapped to GC>=50% regions mapped elsewhere.
      • 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

      • TargetMetrics

        public TargetMetrics()