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 | Description |
---|---|---|
double |
AT_DROPOUT |
A measure of how undercovered <= 50% GC regions are relative to the mean.
|
double |
BAIT_DESIGN_EFFICIENCY |
The ratio of TARGET_TERRITORY/BAIT_TERRITORY.
|
String |
BAIT_SET |
The name of the bait set used in the hybrid selection.
|
long |
BAIT_TERRITORY |
The number of bases which are localized to one or more baits.
|
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.
|
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 a target region.
|
double |
MEDIAN_TARGET_COVERAGE |
The median coverage of a target region.
|
long |
NEAR_BAIT_BASES |
The number of PF_BASES_ALIGNED that are mapped to within a fixed interval containing a baited region, but not within the baited section per se.
|
long |
OFF_BAIT_BASES |
The number of PF_BASES_ALIGNED that are mapped away from any baited region.
|
long |
ON_BAIT_BASES |
The number of PF_BASES_ALIGNED that are mapped to the baited regions of the genome.
|
double |
ON_BAIT_VS_SELECTED |
The fraction of bases on or near baits that are covered by baits, ON_BAIT_BASES/(ON_BAIT_BASES + NEAR_BAIT_BASES).
|
long |
ON_TARGET_BASES |
The number of PF_BASES_ALIGNED that are 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 fraction of PF_BASES_ALIGNED that are mapped away from any baited region, OFF_BAIT_BASES/PF_BASES_ALIGNED.
|
double |
PCT_PF_READS |
The fraction of reads passing the vendor's filter, PF_READS/TOTAL_READS.
|
double |
PCT_PF_UQ_READS |
The fraction of PF_UNIQUE_READS from the TOTAL_READS, PF_UNIQUE_READS/TOTAL_READS.
|
double |
PCT_PF_UQ_READS_ALIGNED |
The fraction of PF_UQ_READS_ALIGNED from the total number of PF reads.
|
double |
PCT_SELECTED_BASES |
The fraction of PF_BASES_ALIGNED located on or near a baited region (ON_BAIT_BASES + NEAR_BAIT_BASES)/PF_BASES_ALIGNED.
|
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.
|
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 all of the PF bases available.
|
long |
PF_BASES_ALIGNED |
The number of PF unique bases that are aligned to the reference genome with mapping scores > 0.
|
long |
PF_READS |
The total 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_UQ_READS_ALIGNED reads.
|
long |
PF_UQ_READS_ALIGNED |
The number of PF_UNIQUE_READS that aligned to the reference genome with a mapping score > 0.
|
long |
TARGET_TERRITORY |
The unique number of target bases in the experiment, where the target sequence is usually exons etc.
|
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 |
---|---|
HsMetrics() |
public 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 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