picard.analysis.directed

## Class TargetedPcrMetrics

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

-     public class TargetedPcrMetrics
      extends MultilevelMetrics

  Metrics class for the analysis of reads obtained from targeted pcr experiments e.g. the TruSeq Custom Amplicon (TSCA) kit (Illumina).

- - ### Field Summary

    Fields
    Modifier and Type | Field and Description
    --- | ---
    `long` | `AMPLICON_TERRITORY` The number of unique bases covered by the intervals of all amplicons in the amplicon set
    `double` | `AT_DROPOUT` A measure of how regions with low GC content (<= 50%), are undercovered relative to mean coverage.
    `String` | `CUSTOM_AMPLICON_SET` The name of the amplicon set used in this metrics collection run
    `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 amplicon region has been amplified above genomic background.
    `double` | `GC_DROPOUT` A measure of how regions of high GC content (>= 50% GC) are undercovered relative to the mean coverage value.
    `long` | `GENOME_SIZE` The number of bases in the reference genome used for alignment
    `double` | `HET_SNP_Q` The Q Score of the theoretical HET SNP sensitivity.
    `double` | `HET_SNP_SENSITIVITY` The theoretical HET SNP sensitivity.
    `double` | `MEAN_AMPLICON_COVERAGE` The mean read coverage of all amplicon regions in the experiment.
    `double` | `MEAN_TARGET_COVERAGE` The mean read coverage of all target regions in an experiment.
    `double` | `MEDIAN_TARGET_COVERAGE` The median coverage of reads that mapped to target regions of an experiment.
    `long` | `NEAR_AMPLICON_BASES` The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region.
    `long` | `OFF_AMPLICON_BASES` The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon.
    `long` | `ON_AMPLICON_BASES` The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome.
    `double` | `ON_AMPLICON_VS_SELECTED` The fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES)
    `long` | `ON_TARGET_BASES` The number of PF_BASES_ALIGNED that mapped to a targeted region of the genome.
    `long` | `ON_TARGET_FROM_PAIR_BASES` The number of bases from PF_SELECTED_UNIQUE_PAIRS that mapped to a targeted region of the genome.
    `double` | `PCT_AMPLIFIED_BASES` The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED.
    `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 bases that were filtered out because they did not map to a base within a target region.
    `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_AMPLICON` The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNED
    `double` | `PCT_PF_READS` The fraction of reads passing filter, PF_READS/TOTAL_READS.
    `double` | `PCT_PF_UQ_READS` The fraction of TOTAL_READS that are unique, PF, and are not duplicates, PF_UNIQUE_READS/TOTAL_READS
    `double` | `PCT_PF_UQ_READS_ALIGNED` Fraction of PF_READS that are unique and align to the reference genome, PF_UQ_READS_ALIGNED/PF_READS
    `double` | `PCT_TARGET_BASES_10X` The fraction of all target bases achieving 10X or greater coverage depth.
    `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 depth.
    `double` | `PCT_TARGET_BASES_2X` The fraction of all target bases achieving 2X or greater coverage depth.
    `double` | `PCT_TARGET_BASES_30X` The fraction of all target bases achieving 30X or greater coverage depth.
    `long` | `PF_BASES` The total number of bases within the PF_READS of the SAM or BAM file to be examined
    `long` | `PF_BASES_ALIGNED` The number of bases from PF_READS that align to the reference genome with mapping score > 0
    `long` | `PF_READS` The total number of reads passing filter (PF), where the filter(s) can be platform/vendor quality controls
    `long` | `PF_SELECTED_PAIRS` Tracks the number of PF read pairs (used to calculate library size)
    `long` | `PF_SELECTED_UNIQUE_PAIRS` Tracks the number of unique, PF, read pairs, observed (used to calculate library size)
    `long` | `PF_UNIQUE_READS` The number of PF_READS that were not marked as sample or optical duplicates.
    `long` | `PF_UQ_BASES_ALIGNED` The number of bases from PF_UNIQUE_READS that align to the reference genome and have a mapping score > 0
    `long` | `PF_UQ_READS_ALIGNED` The total number of PF_UNIQUE_READS that align to the reference genome with mapping scores > 0
    `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 and Description
    `TargetedPcrMetrics()`

  - ### 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

    - #### CUSTOM_AMPLICON_SET

          public String CUSTOM_AMPLICON_SET

      The name of the amplicon set used in this metrics collection run

    - #### GENOME_SIZE

          public long GENOME_SIZE

      The number of bases in the reference genome used for alignment

    - #### AMPLICON_TERRITORY

          public long AMPLICON_TERRITORY

      The number of unique bases covered by the intervals of all amplicons in the amplicon set

    - #### TARGET_TERRITORY

          public long TARGET_TERRITORY

      The number of unique bases covered by the intervals of all targets that should be covered

    - #### 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 passing filter (PF), where the filter(s) can be platform/vendor quality controls

    - #### PF_BASES

          public long PF_BASES

      The total number of bases within the PF_READS of the SAM or BAM file to be examined

    - #### PF_UNIQUE_READS

          public long PF_UNIQUE_READS

      The number of PF_READS that were not marked as sample or optical duplicates.

    - #### 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 TOTAL_READS that are unique, PF, and are not duplicates, PF_UNIQUE_READS/TOTAL_READS

    - #### PF_UQ_READS_ALIGNED

          public long PF_UQ_READS_ALIGNED

      The total number of PF_UNIQUE_READS that align to the reference genome with mapping scores > 0

    - #### PF_SELECTED_PAIRS

          public long PF_SELECTED_PAIRS

      Tracks the number of PF read pairs (used to calculate library size)

    - #### PF_SELECTED_UNIQUE_PAIRS

          public long PF_SELECTED_UNIQUE_PAIRS

      Tracks the number of unique, PF, read pairs, observed (used to calculate library size)

    - #### PCT_PF_UQ_READS_ALIGNED

          public double PCT_PF_UQ_READS_ALIGNED

      Fraction of PF_READS that are unique and align to the reference genome, PF_UQ_READS_ALIGNED/PF_READS

    - #### PF_BASES_ALIGNED

          public long PF_BASES_ALIGNED

      The number of bases from PF_READS that align to the reference genome with mapping score > 0

    - #### PF_UQ_BASES_ALIGNED

          public long PF_UQ_BASES_ALIGNED

      The number of bases from PF_UNIQUE_READS that align to the reference genome and have a mapping score > 0

    - #### ON_AMPLICON_BASES

          public long ON_AMPLICON_BASES

      The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome.

    - #### NEAR_AMPLICON_BASES

          public long NEAR_AMPLICON_BASES

      The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region.

    - #### OFF_AMPLICON_BASES

          public long OFF_AMPLICON_BASES

      The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon.

    - #### ON_TARGET_BASES

          public long ON_TARGET_BASES

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

    - #### ON_TARGET_FROM_PAIR_BASES

          public long ON_TARGET_FROM_PAIR_BASES

      The number of bases from PF_SELECTED_UNIQUE_PAIRS that mapped to a targeted region of the genome.

    - #### PCT_AMPLIFIED_BASES

          public double PCT_AMPLIFIED_BASES

      The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED.

    - #### PCT_OFF_AMPLICON

          public double PCT_OFF_AMPLICON

      The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNED

    - #### ON_AMPLICON_VS_SELECTED

          public double ON_AMPLICON_VS_SELECTED

      The fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES)

    - #### MEAN_AMPLICON_COVERAGE

          public double MEAN_AMPLICON_COVERAGE

      The mean read coverage of all amplicon regions in the experiment.

    - #### MEAN_TARGET_COVERAGE

          public double MEAN_TARGET_COVERAGE

      The mean read coverage of all target regions in an experiment.

    - #### MEDIAN_TARGET_COVERAGE

          public double MEDIAN_TARGET_COVERAGE

      The median coverage of reads that mapped to target regions of an experiment.

    - #### FOLD_ENRICHMENT

          public double FOLD_ENRICHMENT

      The fold by which the amplicon 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 bases that were filtered out because they did not map to a base within a target region.

    - #### 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 depth.

    - #### PCT_TARGET_BASES_10X

          public double PCT_TARGET_BASES_10X

      The fraction of all target bases achieving 10X or greater coverage depth.

    - #### PCT_TARGET_BASES_20X

          public double PCT_TARGET_BASES_20X

      The fraction of all target bases achieving 20X or greater coverage depth.

    - #### PCT_TARGET_BASES_30X

          public double PCT_TARGET_BASES_30X

      The fraction of all target bases achieving 30X or greater coverage depth.

    - #### AT_DROPOUT

          public double AT_DROPOUT

      A measure of how regions with low GC content (<= 50%), are undercovered relative to mean coverage. After binning the GC content [0..50], we calculate a = fraction of target territory, and b = fraction of aligned reads aligned to these targets for each bin. AT DROPOUT is then abs(sum(a-b when a-b < 0)). For example, if the AT_DROPOUT 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 regions of high GC content (>= 50% GC) are undercovered relative to the mean coverage value. 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)). For example, 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 Q Score of the theoretical HET SNP sensitivity.

  - ### Constructor Detail

    - #### TargetedPcrMetrics

          public TargetedPcrMetrics()