Package picard.analysis.directed
Class TargetedPcrMetrics
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- htsjdk.samtools.metrics.MetricBase
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- picard.metrics.MultilevelMetrics
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- picard.analysis.directed.TargetedPcrMetrics
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public class TargetedPcrMetrics extends MultilevelMetrics
Metrics class for the analysis of reads obtained from targeted pcr experiments e.g. the TruSeq Custom Amplicon (TSCA) kit (Illumina).
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Field Summary
Fields Modifier and Type Field Description long
AMPLICON_TERRITORY
The number of unique bases covered by the intervals of all amplicons in the amplicon setdouble
AT_DROPOUT
A measure of how regions with low GC content (<= 50%), are undercovered relative to mean coverage.String
CUSTOM_AMPLICON_SET
The name of the amplicon set used in this metrics collection rundouble
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 amplicon region has been amplified above genomic background.double
GC_DROPOUT
A measure of how regions of high GC content (>= 50% GC) are undercovered relative to the mean coverage value.long
GENOME_SIZE
The number of bases in the reference genome used for alignmentdouble
HET_SNP_Q
The 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_AMPLICON_COVERAGE
The mean read coverage of all amplicon regions in the experiment.double
MEAN_TARGET_COVERAGE
The mean read coverage of all target regions in an experiment.double
MEDIAN_TARGET_COVERAGE
The median coverage of reads that mapped to target regions of an experiment.long
NEAR_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region.long
OFF_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon.long
ON_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome.double
ON_AMPLICON_VS_SELECTED
The fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES)long
ON_TARGET_BASES
The number of PF_BASES_ALIGNED that mapped to a targeted region of the genome.long
ON_TARGET_FROM_PAIR_BASES
The number of bases from PF_SELECTED_UNIQUE_PAIRS that mapped to a targeted region of the genome.double
PCT_AMPLIFIED_BASES
The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED.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 bases that were filtered out because they did not map to a base within a target region.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_AMPLICON
The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNEDdouble
PCT_PF_READS
The fraction of reads passing filter, PF_READS/TOTAL_READS.double
PCT_PF_UQ_READS
The fraction of TOTAL_READS that are unique, PF, and are not duplicates, PF_UNIQUE_READS/TOTAL_READSdouble
PCT_PF_UQ_READS_ALIGNED
Fraction of PF_READS that are unique and align to the reference genome, PF_UQ_READS_ALIGNED/PF_READSdouble
PCT_TARGET_BASES_10X
The fraction of all target bases achieving 10X or greater coverage depth.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 depth.double
PCT_TARGET_BASES_2X
The fraction of all target bases achieving 2X or greater coverage depth.double
PCT_TARGET_BASES_30X
The fraction of all target bases achieving 30X or greater coverage depth.long
PF_BASES
The total number of bases within the PF_READS of the SAM or BAM file to be examinedlong
PF_BASES_ALIGNED
The number of bases from PF_READS that align to the reference genome with mapping score > 0long
PF_READS
The total number of reads passing filter (PF), where the filter(s) can be platform/vendor quality controlslong
PF_SELECTED_PAIRS
Tracks the number of PF read pairs (used to calculate library size)long
PF_SELECTED_UNIQUE_PAIRS
Tracks the number of unique, PF, read pairs, observed (used to calculate library size)long
PF_UNIQUE_READS
The number of PF_READS that were not marked as sample or optical duplicates.long
PF_UQ_BASES_ALIGNED
The number of bases from PF_UNIQUE_READS that align to the reference genome and have a mapping score > 0long
PF_UQ_READS_ALIGNED
The total number of PF_UNIQUE_READS that align to the reference genome with mapping scores > 0long
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 examineddouble
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 TargetedPcrMetrics()
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Field Detail
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CUSTOM_AMPLICON_SET
public String CUSTOM_AMPLICON_SET
The name of the amplicon set used in this metrics collection run
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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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AMPLICON_TERRITORY
public long AMPLICON_TERRITORY
The number of unique bases covered by the intervals of all amplicons in the amplicon 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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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 passing filter (PF), where the filter(s) can be platform/vendor quality controls
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PF_BASES
public long PF_BASES
The total number of bases within the PF_READS of the SAM or BAM file to be examined
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PF_UNIQUE_READS
public long PF_UNIQUE_READS
The number of PF_READS that were not marked as sample or optical duplicates.
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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 TOTAL_READS that are unique, PF, and are not duplicates, PF_UNIQUE_READS/TOTAL_READS
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PF_UQ_READS_ALIGNED
public long PF_UQ_READS_ALIGNED
The total number of PF_UNIQUE_READS that align to the reference genome with mapping scores > 0
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PF_SELECTED_PAIRS
public long PF_SELECTED_PAIRS
Tracks the number of PF read pairs (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, read pairs, observed (used to calculate library size)
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PCT_PF_UQ_READS_ALIGNED
public double PCT_PF_UQ_READS_ALIGNED
Fraction of PF_READS that are unique and align to the reference genome, PF_UQ_READS_ALIGNED/PF_READS
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PF_BASES_ALIGNED
public long PF_BASES_ALIGNED
The number of bases from PF_READS that align to the reference genome with mapping score > 0
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PF_UQ_BASES_ALIGNED
public long PF_UQ_BASES_ALIGNED
The number of bases from PF_UNIQUE_READS that align to the reference genome and have a mapping score > 0
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ON_AMPLICON_BASES
public long ON_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped to an amplified region of the genome.
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NEAR_AMPLICON_BASES
public long NEAR_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped to within a fixed interval of an amplified region, but not on a baited region.
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OFF_AMPLICON_BASES
public long OFF_AMPLICON_BASES
The number of PF_BASES_ALIGNED that mapped neither on or near an amplicon.
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ON_TARGET_BASES
public long ON_TARGET_BASES
The number of PF_BASES_ALIGNED 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 bases from PF_SELECTED_UNIQUE_PAIRS that mapped to a targeted region of the genome.
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PCT_AMPLIFIED_BASES
public double PCT_AMPLIFIED_BASES
The fraction of PF_BASES_ALIGNED that mapped to or near an amplicon, (ON_AMPLICON_BASES + NEAR_AMPLICON_BASES)/PF_BASES_ALIGNED.
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PCT_OFF_AMPLICON
public double PCT_OFF_AMPLICON
The fraction of PF_BASES_ALIGNED that mapped neither onto or near an amplicon, OFF_AMPLICON_BASES/PF_BASES_ALIGNED
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ON_AMPLICON_VS_SELECTED
public double ON_AMPLICON_VS_SELECTED
The fraction of bases mapping to regions on or near amplicons, which mapped directly to but not near amplicons, ON_AMPLICON_BASES/(NEAR_AMPLICON_BASES + ON_AMPLICON_BASES)
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MEAN_AMPLICON_COVERAGE
public double MEAN_AMPLICON_COVERAGE
The mean read coverage of all amplicon regions in the experiment.
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MEAN_TARGET_COVERAGE
public double MEAN_TARGET_COVERAGE
The mean read coverage of all target regions in an experiment.
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MEDIAN_TARGET_COVERAGE
public double MEDIAN_TARGET_COVERAGE
The median coverage of reads that mapped to target regions of an experiment.
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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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FOLD_ENRICHMENT
public double FOLD_ENRICHMENT
The fold by which the amplicon 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 bases that were filtered out because they did not map to a base within a target region.
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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 depth.
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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 depth.
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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 depth.
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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 depth.
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AT_DROPOUT
public double AT_DROPOUT
A measure of how regions with low GC content (<= 50%), are undercovered relative to mean coverage. After binning the GC content [0..50], we calculate a = fraction of target territory, and b = fraction of aligned reads aligned to these targets for each bin. AT DROPOUT is then abs(sum(a-b when a-b < 0)). For example, if the AT_DROPOUT 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 regions of high GC content (>= 50% GC) are undercovered relative to the mean coverage value. 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)). For example, 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 Q Score of the theoretical HET SNP sensitivity.
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