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:
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
Target terrirtoy / bait territory.
|
java.lang.String |
BAIT_SET
The name of the bait set used in the hybrid selection.
|
long |
BAIT_TERRITORY
The number of bases which have one or more baits on top of them.
|
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.
|
java.lang.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 targets.
|
double |
MEDIAN_TARGET_COVERAGE
The median coverage of targets.
|
long |
NEAR_BAIT_BASES
The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region.
|
long |
OFF_BAIT_BASES
The number of PF aligned bases that mapped to neither on or near a bait.
|
long |
ON_BAIT_BASES
The number of PF aligned bases that mapped to a baited region of the genome.
|
double |
ON_BAIT_VS_SELECTED
The percentage of on+near bait 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.
|
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 percentage of aligned PF bases that mapped neither on or near a bait.
|
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_SELECTED_BASES
On+Near Bait Bases / PF Bases Aligned.
|
double |
PCT_TARGET_BASES_100X
The percentage of all target bases achieving 100X or greater coverage.
|
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.
|
double |
PCT_TARGET_BASES_40X
The percentage of all target bases achieving 40X or greater coverage.
|
double |
PCT_TARGET_BASES_50X
The percentage 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 the PF bases available.
|
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_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 aligned reads that are mapped to a reference base.
|
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 unique number of target bases in the experiment where target is usually exons etc.
|
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.
|
LIBRARY, READ_GROUP, SAMPLE
Constructor and Description |
---|
HsMetrics() |
public java.lang.String BAIT_SET
public long GENOME_SIZE
public long BAIT_TERRITORY
public long TARGET_TERRITORY
public double BAIT_DESIGN_EFFICIENCY
public long TOTAL_READS
public long PF_READS
public long PF_UNIQUE_READS
public double PCT_PF_READS
public double PCT_PF_UQ_READS
public long PF_UQ_READS_ALIGNED
public double PCT_PF_UQ_READS_ALIGNED
public long PF_BASES_ALIGNED
public long PF_UQ_BASES_ALIGNED
public long ON_BAIT_BASES
public long NEAR_BAIT_BASES
public long OFF_BAIT_BASES
public long ON_TARGET_BASES
public double PCT_SELECTED_BASES
public double PCT_OFF_BAIT
public double ON_BAIT_VS_SELECTED
public double MEAN_BAIT_COVERAGE
public double MEAN_TARGET_COVERAGE
public double MEDIAN_TARGET_COVERAGE
public double PCT_USABLE_BASES_ON_BAIT
public double PCT_USABLE_BASES_ON_TARGET
public double FOLD_ENRICHMENT
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 java.lang.Long HS_LIBRARY_SIZE
public double HS_PENALTY_10X
public double HS_PENALTY_20X
public double HS_PENALTY_30X
public double HS_PENALTY_40X
public double HS_PENALTY_50X
public double HS_PENALTY_100X
public double AT_DROPOUT
public double GC_DROPOUT
public double HET_SNP_SENSITIVITY
public double HET_SNP_Q