Class PanelMetricsBase

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.metrics.MultilevelMetrics
picard.analysis.directed.PanelMetricsBase
Direct Known Subclasses:
HsMetrics, TargetMetricsBase

public class PanelMetricsBase extends MultilevelMetrics
A base class for Metrics for targeted panels. Metrics for library construction protocols based on PCR amplicons/probes and Hybrid Selection baits are derived from this class.
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    double
    A measure of how undercovered invalid input: '<'= 50% GC regions are relative to the mean.
    double
    The fold over-coverage necessary to raise 80% of bases in "non-zero-cvg" targets to the mean coverage level in those targets.
    double
    A measure of how undercovered >= 50% GC regions are relative to the mean.
    long
    The number of bases in the reference genome used for alignment.
    double
    The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
    double
    The theoretical HET SNP sensitivity.
    long
    The maximum coverage of reads that mapped to target regions of an experiment.
    double
    The mean coverage of targets.
    double
    The median coverage of targets.
    long
    The minimum coverage of reads that mapped to target regions of an experiment.
    long
    The number of PF aligned bases that mapped to a targeted region of the genome.
    double
    The fraction of aligned bases in reads that have MQ=0 and whose 5' end consists of adapter sequence.
    double
    The fraction of aligned bases that were filtered out because they were of low base quality.
    double
    The fraction of aligned bases that were filtered out because they were in reads marked as duplicates.
    double
    The fraction of aligned bases that were filtered out because they were in reads with low mapping quality.
    double
    The fraction of aligned bases that were filtered out because they did not align over a target base.
    double
    The fraction of aligned bases that were filtered out because they were the second observation from an insert with overlapping reads.
    double
    The fraction of reads passing filter, PF_READS/TOTAL_READS.
    double
    The fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS.
    double
    The fraction of unique reads passing filter that align to the reference, PF_UQ_READS_ALIGNED/PF_UNIQUE_READS.
    double
    The fraction of all target bases achieving 100000X or greater coverage.
    double
    The fraction of all target bases achieving 10000X or greater coverage.
    double
    The fraction of all target bases achieving 1000X or greater coverage.
    double
    The fraction of all target bases achieving 100X or greater coverage.
    double
    The fraction of all target bases achieving 10X or greater coverage.
    double
    The fraction of all target bases achieving 1X or greater coverage.
    double
    The fraction of all target bases achieving 20X or greater coverage.
    double
    The fraction of all target bases achieving 25000X or greater coverage.
    double
    The fraction of all target bases achieving 2500X or greater coverage.
    double
    The fraction of all target bases achieving 250X or greater coverage.
    double
    The fraction of all target bases achieving 2X or greater coverage.
    double
    The fraction of all target bases achieving 30X or greater coverage.
    double
    The fraction of all target bases achieving 40X or greater coverage.
    double
    The fraction of all target bases achieving 50000X or greater coverage.
    double
    The fraction of all target bases achieving 5000X or greater coverage.
    double
    The fraction of all target bases achieving 500X or greater coverage.
    double
    The fraction of all target bases achieving 50X or greater coverage.
    long
    The number of bases in the PF_READS of a SAM or BAM file
    long
    The number of PF_BASES that are aligned with mapping score > 0 to the reference genome.
    long
    The number of passing filter reads (PF).
    long
    The number of PF_READS that are not marked as duplicates.
    long
    The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
    long
    The number of PF_UNIQUE_READS that are aligned with mapping score > 0 to the reference genome.
    long
    The number of unique bases covered by the intervals of all targets that should be covered
    long
    The total number of reads in the SAM or BAM file examined.
    double
    The fraction of targets that did not reach coverage=1 over any base.

    Fields inherited from class picard.metrics.MultilevelMetrics

    LIBRARY, READ_GROUP, SAMPLE
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Methods inherited from class htsjdk.samtools.metrics.MetricBase

    equals, hashCode, toString

    Methods inherited from class java.lang.Object

    clone, finalize, getClass, notify, notifyAll, wait, wait, wait
  • Field Details

    • 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_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_TARGET_BASES

      public long ON_TARGET_BASES
      The number of PF aligned bases that mapped 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.
    • 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.
    • MIN_TARGET_COVERAGE

      public long MIN_TARGET_COVERAGE
      The minimum 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_ADAPTER

      public double PCT_EXC_ADAPTER
      The fraction of aligned bases in reads that have MQ=0 and whose 5' end consists of adapter sequence.
    • 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.
    • PCT_TARGET_BASES_250X

      public double PCT_TARGET_BASES_250X
      The fraction of all target bases achieving 250X or greater coverage.
    • PCT_TARGET_BASES_500X

      public double PCT_TARGET_BASES_500X
      The fraction of all target bases achieving 500X or greater coverage.
    • PCT_TARGET_BASES_1000X

      public double PCT_TARGET_BASES_1000X
      The fraction of all target bases achieving 1000X or greater coverage.
    • PCT_TARGET_BASES_2500X

      public double PCT_TARGET_BASES_2500X
      The fraction of all target bases achieving 2500X or greater coverage.
    • PCT_TARGET_BASES_5000X

      public double PCT_TARGET_BASES_5000X
      The fraction of all target bases achieving 5000X or greater coverage.
    • PCT_TARGET_BASES_10000X

      public double PCT_TARGET_BASES_10000X
      The fraction of all target bases achieving 10000X or greater coverage.
    • PCT_TARGET_BASES_25000X

      public double PCT_TARGET_BASES_25000X
      The fraction of all target bases achieving 25000X or greater coverage.
    • PCT_TARGET_BASES_50000X

      public double PCT_TARGET_BASES_50000X
      The fraction of all target bases achieving 50000X or greater coverage.
    • PCT_TARGET_BASES_100000X

      public double PCT_TARGET_BASES_100000X
      The fraction of all target bases achieving 100000X or greater coverage.
    • AT_DROPOUT

      public double AT_DROPOUT
      A measure of how undercovered invalid input: '<'= 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 sum(a-b if a-b > 0 else 0). E.g. if the value is 5%, this implies that 5% of total reads that should have mapped to GCinvalid input: '<'=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 sum(a-b if a-b > 0 else 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 Details

    • PanelMetricsBase

      public PanelMetricsBase()