Package picard.analysis.directed

## 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` | `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` | `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_TARGET_COVERAGE` | The mean coverage of targets.
    `double` | `MEDIAN_TARGET_COVERAGE` | The median coverage of targets.
    `long` | `MIN_TARGET_COVERAGE` | The minimum coverage of reads that mapped to target regions of an experiment.
    `long` | `ON_TARGET_BASES` | The number of PF aligned bases that mapped to a targeted region of the genome.
    `double` | `PCT_EXC_ADAPTER` | The fraction of aligned bases in reads that have MQ=0 and whose 5' end consists of adapter sequence.
    `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_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_TARGET_BASES_100000X` | The fraction of all target bases achieving 100000X or greater coverage.
    `double` | `PCT_TARGET_BASES_10000X` | The fraction of all target bases achieving 10000X or greater coverage.
    `double` | `PCT_TARGET_BASES_1000X` | The fraction of all target bases achieving 1000X or greater coverage.
    `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_25000X` | The fraction of all target bases achieving 25000X or greater coverage.
    `double` | `PCT_TARGET_BASES_2500X` | The fraction of all target bases achieving 2500X or greater coverage.
    `double` | `PCT_TARGET_BASES_250X` | The fraction of all target bases achieving 250X 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_50000X` | The fraction of all target bases achieving 50000X or greater coverage.
    `double` | `PCT_TARGET_BASES_5000X` | The fraction of all target bases achieving 5000X or greater coverage.
    `double` | `PCT_TARGET_BASES_500X` | The fraction of all target bases achieving 500X 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_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.
    `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.

    - ### Fields inherited from class picard.metrics.MultilevelMetrics

      `LIBRARY, READ_GROUP, SAMPLE`

  - ### Constructor Summary

    Constructors
    Constructor | Description
    --- | ---
    `PanelMetricsBase()` |

  - ### 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 Detail

    - #### 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 <= 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

    - #### PanelMetricsBase

          public PanelMetricsBase()