Package picard.analysis.directed
Class HsMetrics
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- htsjdk.samtools.metrics.MetricBase
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- picard.metrics.MultilevelMetrics
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- picard.analysis.directed.HsMetrics
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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:
- Basic sequencing metrics that are either generated as a baseline against which to evaluate other metrics or because they are used in the calculation of other metrics. This includes things like the genome size, the number of reads, the number of aligned reads etc.
- Metrics that are intended for evaluating the performance of the wet-lab assay that generated the data. This group includes metrics like the number of bases mapping on/off/near baits, %selected, fold 80 base penalty, hs library size and the hs penalty metrics. These metrics are calculated prior to some of the filters are applied (e.g. low mapping quality reads, low base quality bases and bases overlapping in the middle of paired-end reads are all counted).
- Metrics for assessing target coverage as a proxy for how well the data is likely to perform in downstream applications like variant calling. This group includes metrics like mean target coverage, the percentage of bases reaching various coverage levels, and the percentage of bases excluded by various filters. These metrics are computed using the strictest subset of the data, after all filters have been applied.
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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
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.long
MAX_TARGET_COVERAGE
The maximum coverage of reads that mapped to target regions of an experiment.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.-
Fields inherited from class picard.metrics.MultilevelMetrics
LIBRARY, READ_GROUP, SAMPLE
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Constructor Summary
Constructors Constructor Description HsMetrics()
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Field Detail
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BAIT_SET
public String BAIT_SET
The name of the bait set used in the hybrid selection.
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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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BAIT_TERRITORY
public long BAIT_TERRITORY
The number of bases which are localized to one or more baits.
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TARGET_TERRITORY
public long TARGET_TERRITORY
The unique number of target bases in the experiment, where the target sequence is usually exons etc.
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BAIT_DESIGN_EFFICIENCY
public double BAIT_DESIGN_EFFICIENCY
The ratio of TARGET_TERRITORY/BAIT_TERRITORY. A value of 1 indicates a perfect design efficiency, while a valud of 0.5 indicates that half of bases within the bait region are not within the target region.
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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 total number of reads that pass the vendor's filter.
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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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PCT_PF_READS
public double PCT_PF_READS
The fraction of reads passing the vendor's filter, PF_READS/TOTAL_READS.
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PCT_PF_UQ_READS
public double PCT_PF_UQ_READS
The fraction of PF_UNIQUE_READS from the TOTAL_READS, PF_UNIQUE_READS/TOTAL_READS.
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PF_UQ_READS_ALIGNED
public long PF_UQ_READS_ALIGNED
The number of PF_UNIQUE_READS that aligned to the reference genome with a mapping score > 0.
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PCT_PF_UQ_READS_ALIGNED
public double PCT_PF_UQ_READS_ALIGNED
The fraction of PF_UQ_READS_ALIGNED from the total number of PF reads.
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PF_BASES_ALIGNED
public long PF_BASES_ALIGNED
The number of PF unique bases that are aligned to the reference genome with mapping scores > 0.
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PF_UQ_BASES_ALIGNED
public long PF_UQ_BASES_ALIGNED
The number of bases in the PF_UQ_READS_ALIGNED reads. Accounts for clipping and gaps.
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ON_BAIT_BASES
public long ON_BAIT_BASES
The number of PF_BASES_ALIGNED that are mapped to the baited regions of the genome.
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NEAR_BAIT_BASES
public 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.
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OFF_BAIT_BASES
public long OFF_BAIT_BASES
The number of PF_BASES_ALIGNED that are mapped away from any baited region.
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ON_TARGET_BASES
public long ON_TARGET_BASES
The number of PF_BASES_ALIGNED that are mapped to a targeted region of the genome.
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PCT_SELECTED_BASES
public 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.
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PCT_OFF_BAIT
public double PCT_OFF_BAIT
The fraction of PF_BASES_ALIGNED that are mapped away from any baited region, OFF_BAIT_BASES/PF_BASES_ALIGNED.
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ON_BAIT_VS_SELECTED
public 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).
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MEAN_BAIT_COVERAGE
public double MEAN_BAIT_COVERAGE
The mean coverage of all baits in the experiment.
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MEAN_TARGET_COVERAGE
public double MEAN_TARGET_COVERAGE
The mean coverage of a target region.
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MEDIAN_TARGET_COVERAGE
public double MEDIAN_TARGET_COVERAGE
The median coverage of a target region.
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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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PCT_USABLE_BASES_ON_BAIT
public double PCT_USABLE_BASES_ON_BAIT
The number of aligned, de-duped, on-bait bases out of the PF bases available.
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PCT_USABLE_BASES_ON_TARGET
public double PCT_USABLE_BASES_ON_TARGET
The number of aligned, de-duped, on-target bases out of all of the PF bases available.
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FOLD_ENRICHMENT
public double FOLD_ENRICHMENT
The fold by which the baited region has been amplified above genomic background.
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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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HS_LIBRARY_SIZE
public Long HS_LIBRARY_SIZE
The estimated number of unique molecules in the selected part of the library.
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HS_PENALTY_10X
public double HS_PENALTY_10X
The "hybrid selection penalty" incurred to get 80% of target bases to 10X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 10X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 10 * HS_PENALTY_10X.
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HS_PENALTY_20X
public double HS_PENALTY_20X
The "hybrid selection penalty" incurred to get 80% of target bases to 20X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 20X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 20 * HS_PENALTY_20X.
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HS_PENALTY_30X
public double HS_PENALTY_30X
The "hybrid selection penalty" incurred to get 80% of target bases to 30X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 30X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 30 * HS_PENALTY_30X.
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HS_PENALTY_40X
public double HS_PENALTY_40X
The "hybrid selection penalty" incurred to get 80% of target bases to 40X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 40X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 40 * HS_PENALTY_40X.
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HS_PENALTY_50X
public double HS_PENALTY_50X
The "hybrid selection penalty" incurred to get 80% of target bases to 50X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 50X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 50 * HS_PENALTY_50X.
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HS_PENALTY_100X
public double HS_PENALTY_100X
The "hybrid selection penalty" incurred to get 80% of target bases to 100X. This metric should be interpreted as: if I have a design with 10 megabases of target, and want to get 100X coverage I need to sequence until PF_ALIGNED_BASES = 10^7 * 100 * HS_PENALTY_100X.
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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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