public class TargetMetrics extends MultilevelMetrics
| 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 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_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 run
|
long |
PROBE_TERRITORY |
The number of unique bases covered by the intervals of all probes in the probe set
|
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.
|
LIBRARY, READ_GROUP, SAMPLE| Constructor | Description |
|---|---|
TargetMetrics() |
public String PROBE_SET
public long PROBE_TERRITORY
public long TARGET_TERRITORY
public long GENOME_SIZE
public long TOTAL_READS
public long PF_READS
public long PF_BASES
public long PF_UNIQUE_READS
public long PF_SELECTED_PAIRS
public long PF_SELECTED_UNIQUE_PAIRS
public long PF_UQ_READS_ALIGNED
public long PF_BASES_ALIGNED
public long PF_UQ_BASES_ALIGNED
public long ON_PROBE_BASES
public long NEAR_PROBE_BASES
public long OFF_PROBE_BASES
public long ON_TARGET_BASES
public long ON_TARGET_FROM_PAIR_BASES
public double PCT_PF_READS
public double PCT_PF_UQ_READS
public double PCT_PF_UQ_READS_ALIGNED
public double PCT_SELECTED_BASES
public double PCT_OFF_PROBE
public double ON_PROBE_VS_SELECTED
public double MEAN_PROBE_COVERAGE
public double FOLD_ENRICHMENT
public double MEAN_TARGET_COVERAGE
public double MEDIAN_TARGET_COVERAGE
public long MAX_TARGET_COVERAGE
public double ZERO_CVG_TARGETS_PCT
public double PCT_EXC_DUPE
public double PCT_EXC_MAPQ
public double PCT_EXC_BASEQ
public double PCT_EXC_OVERLAP
public double PCT_EXC_OFF_TARGET
public double FOLD_80_BASE_PENALTY
public double PCT_TARGET_BASES_1X
public double PCT_TARGET_BASES_2X
public double PCT_TARGET_BASES_10X
public double PCT_TARGET_BASES_20X
public double PCT_TARGET_BASES_30X
public double PCT_TARGET_BASES_40X
public double PCT_TARGET_BASES_50X
public double PCT_TARGET_BASES_100X
public double AT_DROPOUT
public double GC_DROPOUT
public double HET_SNP_SENSITIVITY
public double HET_SNP_Q