TargetedPcrMetrics (PICARD JDK API Documentation)

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

public class TargetedPcrMetrics
extends MultilevelMetrics

Metrics class for targeted pcr runs such as TSCA runs

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 undercovered <= 50% GC regions are relative to the mean.
`java.lang.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 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 Q Score of the theoretical HET SNP sensitivity.
`double`	`HET_SNP_SENSITIVITY` The theoretical HET SNP sensitivity.
`double`	`MEAN_AMPLICON_COVERAGE` The mean coverage of all amplicons in the experiment.
`double`	`MEAN_TARGET_COVERAGE` The mean coverage of targets.
`double`	`MEDIAN_TARGET_COVERAGE` The median coverage of targets.
`long`	`NEAR_AMPLICON_BASES` The number of PF aligned bases 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 aligned bases that mapped to neither on or near an amplicon.
`long`	`ON_AMPLICON_BASES` The number of PF aligned amplified that mapped to an amplified region of the genome.
`double`	`ON_AMPLICON_VS_SELECTED` The percentage of on+near amplicon bases that are on as opposed to near.
`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_AMPLIFIED_BASES` On+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 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_AMPLICON` The percentage of aligned PF bases that mapped neither on or near an amplicon.
`double`	`PCT_PF_READS` PF reads / total reads.
`double`	`PCT_PF_UQ_READS` PF Unique Reads / Total Reads.
`double`	`PCT_PF_UQ_READS_ALIGNED` PF Reads Aligned / PF Reads.
`double`	`PCT_TARGET_BASES_10X` The percentage of all target bases achieving 10X or greater coverage.
`double`	`PCT_TARGET_BASES_1X` The percentage of all target bases achieving 1X or greater coverage.
`double`	`PCT_TARGET_BASES_20X` The percentage of all target bases achieving 20X or greater coverage.
`double`	`PCT_TARGET_BASES_2X` The percentage of all target bases achieving 2X or greater coverage.
`double`	`PCT_TARGET_BASES_30X` The percentage of all target bases achieving 30X or greater coverage.
`long`	`PF_BASES` THe number of bases in the SAM or BAM file to be examined
`long`	`PF_BASES_ALIGNED` The number of PF unique bases that are aligned with mapping score > 0 to the reference genome.
`long`	`PF_READS` The number of reads that pass the vendor's filter.
`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 reads 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.
`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 examine.
`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()

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 java.lang.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 examine.
  - PF_READS
```
public long PF_READS
```
    The number of reads that pass the vendor's filter.
  - PF_BASES
```
public long PF_BASES
```
    THe number of bases in the SAM or BAM file to be examined
  - 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
```
    PF reads / total reads. The percent of reads passing filter.
  - PCT_PF_UQ_READS
```
public double PCT_PF_UQ_READS
```
    PF Unique Reads / Total Reads.
  - 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_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 reads pairs we see (used to calc library size)
  - PCT_PF_UQ_READS_ALIGNED
```
public double PCT_PF_UQ_READS_ALIGNED
```
    PF Reads Aligned / PF Reads.
  - PF_BASES_ALIGNED
```
public long PF_BASES_ALIGNED
```
    The number of PF unique 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_AMPLICON_BASES
```
public long ON_AMPLICON_BASES
```
    The number of PF aligned amplified that mapped to an amplified region of the genome.
  - NEAR_AMPLICON_BASES
```
public long NEAR_AMPLICON_BASES
```
    The number of PF aligned bases 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 aligned bases that mapped to neither on or near an amplicon.
  - 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_AMPLIFIED_BASES
```
public double PCT_AMPLIFIED_BASES
```
    On+Near Amplicon Bases / PF Bases Aligned.
  - PCT_OFF_AMPLICON
```
public double PCT_OFF_AMPLICON
```
    The percentage of aligned PF bases that mapped neither on or near an amplicon.
  - ON_AMPLICON_VS_SELECTED
```
public double ON_AMPLICON_VS_SELECTED
```
    The percentage of on+near amplicon bases that are on as opposed to near.
  - MEAN_AMPLICON_COVERAGE
```
public double MEAN_AMPLICON_COVERAGE
```
    The mean coverage of all amplicons in the experiment.
  - 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.
  - 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 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 percentage of all target bases achieving 1X or greater coverage.
  - PCT_TARGET_BASES_2X
```
public double PCT_TARGET_BASES_2X
```
    The percentage of all target bases achieving 2X or greater coverage.
  - PCT_TARGET_BASES_10X
```
public double PCT_TARGET_BASES_10X
```
    The percentage of all target bases achieving 10X or greater coverage.
  - PCT_TARGET_BASES_20X
```
public double PCT_TARGET_BASES_20X
```
    The percentage of all target bases achieving 20X or greater coverage.
  - PCT_TARGET_BASES_30X
```
public double PCT_TARGET_BASES_30X
```
    The percentage of all target bases achieving 30X 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 Q Score of the theoretical HET SNP sensitivity.
- Constructor Detail
  - TargetedPcrMetrics
```
public TargetedPcrMetrics()
```

Class TargetedPcrMetrics

Field Summary

Fields inherited from class picard.metrics.MultilevelMetrics

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

Methods inherited from class java.lang.Object

Field Detail

CUSTOM_AMPLICON_SET

GENOME_SIZE

AMPLICON_TERRITORY

TARGET_TERRITORY

TOTAL_READS

PF_READS

PF_BASES

PF_UNIQUE_READS

PCT_PF_READS

PCT_PF_UQ_READS

PF_UQ_READS_ALIGNED

PF_SELECTED_PAIRS

PF_SELECTED_UNIQUE_PAIRS

PCT_PF_UQ_READS_ALIGNED

PF_BASES_ALIGNED

PF_UQ_BASES_ALIGNED

ON_AMPLICON_BASES

NEAR_AMPLICON_BASES

OFF_AMPLICON_BASES

ON_TARGET_BASES

ON_TARGET_FROM_PAIR_BASES

PCT_AMPLIFIED_BASES

PCT_OFF_AMPLICON

ON_AMPLICON_VS_SELECTED

MEAN_AMPLICON_COVERAGE

MEAN_TARGET_COVERAGE

MEDIAN_TARGET_COVERAGE

FOLD_ENRICHMENT

ZERO_CVG_TARGETS_PCT

PCT_EXC_DUPE

PCT_EXC_MAPQ

PCT_EXC_BASEQ

PCT_EXC_OVERLAP

PCT_EXC_OFF_TARGET

FOLD_80_BASE_PENALTY

PCT_TARGET_BASES_1X

PCT_TARGET_BASES_2X

PCT_TARGET_BASES_10X

PCT_TARGET_BASES_20X

PCT_TARGET_BASES_30X

AT_DROPOUT

GC_DROPOUT

HET_SNP_SENSITIVITY

HET_SNP_Q

Constructor Detail

TargetedPcrMetrics