Package picard.analysis.directed
Class TargetMetrics
- java.lang.Object
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- htsjdk.samtools.metrics.MetricBase
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- picard.metrics.MultilevelMetrics
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- picard.analysis.directed.TargetMetrics
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public class TargetMetrics extends MultilevelMetrics
TargetMetrics, are metrics to measure how well we hit specific targets (or baits) when using a targeted sequencing process like hybrid selection or Targeted PCR Techniques (TSCA). TargetMetrics at the moment are the metrics that are shared by both HybridSelection and TargetedPcrMetrics.
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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
FOLD_ENRICHMENT
The fold by which the probed region has been amplified above genomic background, (ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES))/(PROBE_TERRITORY/GENOME_SIZE)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_PROBE_COVERAGE
The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.double
MEAN_TARGET_COVERAGE
The mean coverage of targets.double
MEDIAN_TARGET_COVERAGE
The median coverage of targets.long
NEAR_PROBE_BASES
The number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a baited region.long
OFF_PROBE_BASES
The number of PF aligned bases that mapped to neither on or near a probe.long
ON_PROBE_BASES
The number of PF aligned probed bases that mapped to a baited region of the genome.double
ON_PROBE_VS_SELECTED
The fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES).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_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_PROBE
The fraction of aligned PF bases that mapped neither on or near a probe, OFF_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).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_SELECTED_BASES
The fraction of bases that map on or near a probe (ON_PROBE_BASES + NEAR_PROBE_BASES)/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).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.long
PF_BASES
The number of bases in the PF_READS of a SAM or BAM filelong
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_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_SELECTED_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.String
PROBE_SET
The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection runlong
PROBE_TERRITORY
The number of unique bases covered by the intervals of all probes in the probe setlong
TARGET_TERRITORY
The number of unique bases covered by the intervals of all targets that should be coveredlong
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
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Constructor Summary
Constructors Constructor Description TargetMetrics()
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Field Detail
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PROBE_SET
public String PROBE_SET
The name of the PROBE_SET (BAIT_SET, AMPLICON_SET, ...) used in this metrics collection run
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PROBE_TERRITORY
public long PROBE_TERRITORY
The number of unique bases covered by the intervals of all probes in the probe set
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TARGET_TERRITORY
public long TARGET_TERRITORY
The number of unique bases covered by the intervals of all targets that should be covered
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GENOME_SIZE
public long GENOME_SIZE
The number of bases in the reference genome used for alignment.
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TOTAL_READS
public long TOTAL_READS
The total number of reads in the SAM or BAM file examined.
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PF_READS
public long PF_READS
The number of passing filter reads (PF).
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PF_BASES
public long PF_BASES
The number of bases in the PF_READS of a SAM or BAM file
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PF_UNIQUE_READS
public long PF_UNIQUE_READS
The number of PF_READS that are not marked as duplicates.
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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)
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PF_SELECTED_UNIQUE_PAIRS
public long PF_SELECTED_UNIQUE_PAIRS
Tracks the number of unique PF_SELECTED_PAIRS we see (used to calc library size)
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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.
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PF_BASES_ALIGNED
public long PF_BASES_ALIGNED
The number of PF_BASES that are aligned with mapping score > 0 to the reference genome.
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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.
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ON_PROBE_BASES
public long ON_PROBE_BASES
The number of PF aligned probed bases that mapped to a baited region of the genome.
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NEAR_PROBE_BASES
public long NEAR_PROBE_BASES
The number of PF aligned bases that mapped to within a fixed interval of a probed region, but not on a baited region.
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OFF_PROBE_BASES
public long OFF_PROBE_BASES
The number of PF aligned bases that mapped to neither on or near a probe.
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ON_TARGET_BASES
public long ON_TARGET_BASES
The number of PF aligned bases that mapped to a targeted region of the genome.
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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.
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PCT_PF_READS
public double PCT_PF_READS
The fraction of reads passing filter, PF_READS/TOTAL_READS.
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PCT_PF_UQ_READS
public double PCT_PF_UQ_READS
The fraction of unique reads passing filter, PF_UNIQUE_READS/TOTAL_READS.
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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.
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PCT_SELECTED_BASES
public double PCT_SELECTED_BASES
The fraction of bases that map on or near a probe (ON_PROBE_BASES + NEAR_PROBE_BASES)/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
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PCT_OFF_PROBE
public double PCT_OFF_PROBE
The fraction of aligned PF bases that mapped neither on or near a probe, OFF_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES).
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ON_PROBE_VS_SELECTED
public double ON_PROBE_VS_SELECTED
The fraction of on+near probe bases that are on as opposed to near, ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES).
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MEAN_PROBE_COVERAGE
public double MEAN_PROBE_COVERAGE
The mean coverage of all probes in the experiment, ON_PROBE_BASES/PROBE_TERRITORY.
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FOLD_ENRICHMENT
public double FOLD_ENRICHMENT
The fold by which the probed region has been amplified above genomic background, (ON_PROBE_BASES/(ON_PROBE_BASES + NEAR_PROBE_BASES + OFF_PROBE_BASES))/(PROBE_TERRITORY/GENOME_SIZE)
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MEAN_TARGET_COVERAGE
public double MEAN_TARGET_COVERAGE
The mean coverage of targets.
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MEDIAN_TARGET_COVERAGE
public double MEDIAN_TARGET_COVERAGE
The median coverage of targets.
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MAX_TARGET_COVERAGE
public long MAX_TARGET_COVERAGE
The maximum coverage of reads that mapped to target regions of an experiment.
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ZERO_CVG_TARGETS_PCT
public double ZERO_CVG_TARGETS_PCT
The fraction of targets that did not reach coverage=1 over any base.
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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.
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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.
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PCT_EXC_BASEQ
public double PCT_EXC_BASEQ
The fraction of aligned bases that were filtered out because they were of low base quality.
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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.
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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.
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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.
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PCT_TARGET_BASES_1X
public double PCT_TARGET_BASES_1X
The fraction of all target bases achieving 1X or greater coverage.
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PCT_TARGET_BASES_2X
public double PCT_TARGET_BASES_2X
The fraction of all target bases achieving 2X or greater coverage.
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PCT_TARGET_BASES_10X
public double PCT_TARGET_BASES_10X
The fraction of all target bases achieving 10X or greater coverage.
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PCT_TARGET_BASES_20X
public double PCT_TARGET_BASES_20X
The fraction of all target bases achieving 20X or greater coverage.
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PCT_TARGET_BASES_30X
public double PCT_TARGET_BASES_30X
The fraction of all target bases achieving 30X or greater coverage.
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PCT_TARGET_BASES_40X
public double PCT_TARGET_BASES_40X
The fraction of all target bases achieving 40X or greater coverage.
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PCT_TARGET_BASES_50X
public double PCT_TARGET_BASES_50X
The fraction of all target bases achieving 50X or greater coverage.
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PCT_TARGET_BASES_100X
public double PCT_TARGET_BASES_100X
The fraction of all target bases achieving 100X or greater coverage.
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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.
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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.
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HET_SNP_SENSITIVITY
public double HET_SNP_SENSITIVITY
The theoretical HET SNP sensitivity.
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HET_SNP_Q
public double HET_SNP_Q
The Phred Scaled Q Score of the theoretical HET SNP sensitivity.
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