picard.analysis.directed

## Class HsMetrics

- java.lang.Object
- - htsjdk.samtools.metrics.MetricBase
  - - picard.metrics.MultilevelMetrics
    - - picard.analysis.directed.HsMetrics

-     public class HsMetrics
      extends MultilevelMetrics

  Metrics generated by CollectHsMetrics for the analysis of target-capture sequencing experiments. The metrics in this class fall broadly into three categories:

  - Basic sequencing metrics that are either generated as a baseline against which to evaluate other metrics or because they are used in the calculation of other metrics. This includes things like the genome size, the number of reads, the number of aligned reads etc.
  - Metrics that are intended for evaluating the performance of the wet-lab assay that generated the data. This group includes metrics like the number of bases mapping on/off/near baits, %selected, fold 80 base penalty, hs library size and the hs penalty metrics. These metrics are calculated prior to some of the filters are applied (e.g. low mapping quality reads, low base quality bases and bases overlapping in the middle of paired-end reads are all counted).
  - Metrics for assessing target coverage as a proxy for how well the data is likely to perform in downstream applications like variant calling. This group includes metrics like mean target coverage, the percentage of bases reaching various coverage levels, and the percentage of bases excluded by various filters. These metrics are computed using the strictest subset of the data, after all filters have been applied.

- - ### Field Summary

    Fields
    Modifier and Type | Field and Description
    --- | ---
    `double` | `AT_DROPOUT` A measure of how undercovered <= 50% GC regions are relative to the mean.
    `double` | `BAIT_DESIGN_EFFICIENCY` The ratio of TARGET_TERRITORY/BAIT_TERRITORY.
    `String` | `BAIT_SET` The name of the bait set used in the hybrid selection.
    `long` | `BAIT_TERRITORY` The number of bases which are localized to one or more baits.
    `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 baited region has been amplified above genomic background.
    `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` | `HS_LIBRARY_SIZE` The estimated number of unique molecules in the selected part of the library.
    `double` | `HS_PENALTY_100X` The "hybrid selection penalty" incurred to get 80% of target bases to 100X.
    `double` | `HS_PENALTY_10X` The "hybrid selection penalty" incurred to get 80% of target bases to 10X.
    `double` | `HS_PENALTY_20X` The "hybrid selection penalty" incurred to get 80% of target bases to 20X.
    `double` | `HS_PENALTY_30X` The "hybrid selection penalty" incurred to get 80% of target bases to 30X.
    `double` | `HS_PENALTY_40X` The "hybrid selection penalty" incurred to get 80% of target bases to 40X.
    `double` | `HS_PENALTY_50X` The "hybrid selection penalty" incurred to get 80% of target bases to 50X.
    `double` | `MEAN_BAIT_COVERAGE` The mean coverage of all baits in the experiment.
    `double` | `MEAN_TARGET_COVERAGE` The mean coverage of a target region.
    `double` | `MEDIAN_TARGET_COVERAGE` The median coverage of a target region.
    `long` | `NEAR_BAIT_BASES` The number of PF_BASES_ALIGNED that are mapped to within a fixed interval containing a baited region, but not within the baited section per se.
    `long` | `OFF_BAIT_BASES` The number of PF_BASES_ALIGNED that are mapped away from any baited region.
    `long` | `ON_BAIT_BASES` The number of PF_BASES_ALIGNED that are mapped to the baited regions of the genome.
    `double` | `ON_BAIT_VS_SELECTED` The fraction of bases on or near baits that are covered by baits, ON_BAIT_BASES/(ON_BAIT_BASES + NEAR_BAIT_BASES).
    `long` | `ON_TARGET_BASES` The number of PF_BASES_ALIGNED that are mapped 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_BAIT` The fraction of PF_BASES_ALIGNED that are mapped away from any baited region, OFF_BAIT_BASES/PF_BASES_ALIGNED.
    `double` | `PCT_PF_READS` The fraction of reads passing the vendor's filter, PF_READS/TOTAL_READS.
    `double` | `PCT_PF_UQ_READS` The fraction of PF_UNIQUE_READS from the TOTAL_READS, PF_UNIQUE_READS/TOTAL_READS.
    `double` | `PCT_PF_UQ_READS_ALIGNED` The fraction of PF_UQ_READS_ALIGNED from the total number of PF reads.
    `double` | `PCT_SELECTED_BASES` The fraction of PF_BASES_ALIGNED located on or near a baited region (ON_BAIT_BASES + NEAR_BAIT_BASES)/PF_BASES_ALIGNED.
    `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.
    `double` | `PCT_USABLE_BASES_ON_BAIT` The number of aligned, de-duped, on-bait bases out of the PF bases available.
    `double` | `PCT_USABLE_BASES_ON_TARGET` The number of aligned, de-duped, on-target bases out of all of the PF bases available.
    `long` | `PF_BASES_ALIGNED` The number of PF unique bases that are aligned to the reference genome with mapping scores > 0.
    `long` | `PF_READS` The total number of reads that pass the vendor's filter.
    `long` | `PF_UNIQUE_READS` The number of PF reads that are not marked as duplicates.
    `long` | `PF_UQ_BASES_ALIGNED` The number of bases in the PF_UQ_READS_ALIGNED reads.
    `long` | `PF_UQ_READS_ALIGNED` The number of PF_UNIQUE_READS that aligned to the reference genome with a mapping score > 0.
    `long` | `TARGET_TERRITORY` The unique number of target bases in the experiment, where the target sequence is usually exons etc.
    `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 and Description
    `HsMetrics()`

  - ### 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

    - #### BAIT_SET

          public String BAIT_SET

      The name of the bait set used in the hybrid selection.

    - #### GENOME_SIZE

          public long GENOME_SIZE

      The number of bases in the reference genome used for alignment.

    - #### BAIT_TERRITORY

          public long BAIT_TERRITORY

      The number of bases which are localized to one or more baits.

    - #### TARGET_TERRITORY

          public long TARGET_TERRITORY

      The unique number of target bases in the experiment, where the target sequence is usually exons etc.

    - #### BAIT_DESIGN_EFFICIENCY

          public double BAIT_DESIGN_EFFICIENCY

      The ratio of TARGET_TERRITORY/BAIT_TERRITORY. A value of 1 indicates a perfect design efficiency, while a valud of 0.5 indicates that half of bases within the bait region are not within the target region.

    - #### 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 total number of reads that pass the vendor's filter.

    - #### PF_UNIQUE_READS

          public long PF_UNIQUE_READS

      The number of PF reads that are not marked as duplicates.

    - #### PCT_PF_READS

          public double PCT_PF_READS

      The fraction of reads passing the vendor's filter, PF_READS/TOTAL_READS.

    - #### PCT_PF_UQ_READS

          public double PCT_PF_UQ_READS

      The fraction of PF_UNIQUE_READS from the TOTAL_READS, PF_UNIQUE_READS/TOTAL_READS.

    - #### PF_UQ_READS_ALIGNED

          public long PF_UQ_READS_ALIGNED

      The number of PF_UNIQUE_READS that aligned to the reference genome with a mapping score > 0.

    - #### PCT_PF_UQ_READS_ALIGNED

          public double PCT_PF_UQ_READS_ALIGNED

      The fraction of PF_UQ_READS_ALIGNED from the total number of PF reads.

    - #### PF_BASES_ALIGNED

          public long PF_BASES_ALIGNED

      The number of PF unique bases that are aligned to the reference genome with mapping scores > 0.

    - #### PF_UQ_BASES_ALIGNED

          public long PF_UQ_BASES_ALIGNED

      The number of bases in the PF_UQ_READS_ALIGNED reads. Accounts for clipping and gaps.

    - #### ON_BAIT_BASES

          public long ON_BAIT_BASES

      The number of PF_BASES_ALIGNED that are mapped to the baited regions of the genome.

    - #### NEAR_BAIT_BASES

          public long NEAR_BAIT_BASES

      The number of PF_BASES_ALIGNED that are mapped to within a fixed interval containing a baited region, but not within the baited section per se.

    - #### OFF_BAIT_BASES

          public long OFF_BAIT_BASES

      The number of PF_BASES_ALIGNED that are mapped away from any baited region.

    - #### ON_TARGET_BASES

          public long ON_TARGET_BASES

      The number of PF_BASES_ALIGNED that are mapped to a targeted region of the genome.

    - #### PCT_SELECTED_BASES

          public double PCT_SELECTED_BASES

      The fraction of PF_BASES_ALIGNED located on or near a baited region (ON_BAIT_BASES + NEAR_BAIT_BASES)/PF_BASES_ALIGNED.

    - #### PCT_OFF_BAIT

          public double PCT_OFF_BAIT

      The fraction of PF_BASES_ALIGNED that are mapped away from any baited region, OFF_BAIT_BASES/PF_BASES_ALIGNED.

    - #### ON_BAIT_VS_SELECTED

          public double ON_BAIT_VS_SELECTED

      The fraction of bases on or near baits that are covered by baits, ON_BAIT_BASES/(ON_BAIT_BASES + NEAR_BAIT_BASES).

    - #### MEAN_BAIT_COVERAGE

          public double MEAN_BAIT_COVERAGE

      The mean coverage of all baits in the experiment.

    - #### MEAN_TARGET_COVERAGE

          public double MEAN_TARGET_COVERAGE

      The mean coverage of a target region.

    - #### MEDIAN_TARGET_COVERAGE

          public double MEDIAN_TARGET_COVERAGE

      The median coverage of a target region.

    - #### PCT_USABLE_BASES_ON_BAIT

          public double PCT_USABLE_BASES_ON_BAIT

      The number of aligned, de-duped, on-bait bases out of the PF bases available.

    - #### PCT_USABLE_BASES_ON_TARGET

          public double PCT_USABLE_BASES_ON_TARGET

      The number of aligned, de-duped, on-target bases out of all of the PF bases available.

    - #### FOLD_ENRICHMENT

          public double FOLD_ENRICHMENT

      The fold by which the baited region has been amplified above genomic background.

    - #### 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.

    - #### HS_LIBRARY_SIZE

          public Long HS_LIBRARY_SIZE

      The estimated number of unique molecules in the selected part of the library.

    - #### HS_PENALTY_10X

          public double HS_PENALTY_10X

      The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 10X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 10 * HS_PENALTY_10X.

    - #### HS_PENALTY_20X

          public double HS_PENALTY_20X

      The "hybrid selection penalty" incurred to get 80% of target bases to 20X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 20X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 20 * HS_PENALTY_20X.

    - #### HS_PENALTY_30X

          public double HS_PENALTY_30X

      The "hybrid selection penalty" incurred to get 80% of target bases to 30X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 30X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 30 * HS_PENALTY_30X.

    - #### HS_PENALTY_40X

          public double HS_PENALTY_40X

      The "hybrid selection penalty" incurred to get 80% of target bases to 40X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 40X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 40 * HS_PENALTY_40X.

    - #### HS_PENALTY_50X

          public double HS_PENALTY_50X

      The "hybrid selection penalty" incurred to get 80% of target bases to 50X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 50X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 50 * HS_PENALTY_50X.

    - #### HS_PENALTY_100X

          public double HS_PENALTY_100X

      The "hybrid selection penalty" incurred to get 80% of target bases to 100X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 100X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 100 * HS_PENALTY_100X.

    - #### 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

    - #### HsMetrics

          public HsMetrics()