picard.analysis

Class CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.analysis.CollectWgsMetrics.WgsMetrics

picard.analysis.CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics

Enclosing class:

CollectWgsMetricsFromQuerySorted

public static class CollectWgsMetricsFromQuerySorted.QuerySortedSeqMetrics
extends CollectWgsMetrics.WgsMetrics

Metrics for evaluating the performance of whole genome sequencing experiments.

Field Summary

Fields

Modifier and Type	Field and Description
double	MEAN_INSERT_SIZE The mean insert size, after filters are applied.
long	PF_ADAPTER_READS The number of PF reads that are unaligned and match to a known adapter sequence right from the start of the read.
long	PF_BASES The total number of bases, before any filters are applied.
long	PF_CHIMERIC_PAIRS The number of PF reads that map outside of a maximum insert size (100kb) or that have the two ends mapping to different chromosomes.
long	PF_DUPE_PAIRS The number of duplicate read pairs, before any filters are applied.
long	PF_NOISE_READS The number of PF reads that are marked as noise reads.
long	PF_ORIENTED_PAIRS The number of read pairs with standard orientations from which to calculate mean insert size, after filters are applied.
long	PF_PASSING_BASES The number of passing bases, after all filters are applied.
long	PF_READ_PAIRS The number of read pairs, before all filters are applied.
long	PF_READS_ALIGNED The number of aligned reads, before any filters are applied.
CollectWgsMetricsFromQuerySorted.FILTERING_STRINGENCY	TYPE Identifier for metrics type

Fields inherited from class picard.analysis.CollectWgsMetrics.WgsMetrics

GENOME_TERRITORY, HET_SNP_Q, HET_SNP_SENSITIVITY, MAD_COVERAGE, MEAN_COVERAGE, MEDIAN_COVERAGE, PCT_100X, PCT_10X, PCT_15X, PCT_1X, PCT_20X, PCT_25X, PCT_30X, PCT_40X, PCT_50X, PCT_5X, PCT_60X, PCT_70X, PCT_80X, PCT_90X, PCT_EXC_BASEQ, PCT_EXC_CAPPED, PCT_EXC_DUPE, PCT_EXC_MAPQ, PCT_EXC_OVERLAP, PCT_EXC_TOTAL, PCT_EXC_UNPAIRED, SD_COVERAGE

Constructor Summary

Constructors

Constructor and Description
QuerySortedSeqMetrics()

Method Summary

Methods inherited from class htsjdk.samtools.metrics.MetricBase

equals, hashCode, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Field Detail

TYPE

public CollectWgsMetricsFromQuerySorted.FILTERING_STRINGENCY TYPE

Identifier for metrics type

PF_BASES

public long PF_BASES

The total number of bases, before any filters are applied.

PF_PASSING_BASES

public long PF_PASSING_BASES

The number of passing bases, after all filters are applied.

PF_READ_PAIRS

public long PF_READ_PAIRS

The number of read pairs, before all filters are applied.

PF_DUPE_PAIRS

public long PF_DUPE_PAIRS

The number of duplicate read pairs, before any filters are applied.

PF_READS_ALIGNED

public long PF_READS_ALIGNED

The number of aligned reads, before any filters are applied.

PF_NOISE_READS

public long PF_NOISE_READS

The number of PF reads that are marked as noise reads. A noise read is one which is composed entirely of A bases and/or N bases. These reads are marked as they are usually artifactual and are of no use in downstream analysis.

PF_CHIMERIC_PAIRS

public long PF_CHIMERIC_PAIRS

The number of PF reads that map outside of a maximum insert size (100kb) or that have the two ends mapping to different chromosomes.

PF_ADAPTER_READS

public long PF_ADAPTER_READS

The number of PF reads that are unaligned and match to a known adapter sequence right from the start of the read.

PF_ORIENTED_PAIRS

public long PF_ORIENTED_PAIRS

The number of read pairs with standard orientations from which to calculate mean insert size, after filters are applied.

MEAN_INSERT_SIZE

public double MEAN_INSERT_SIZE

The mean insert size, after filters are applied.

Constructor Detail

QuerySortedSeqMetrics

public QuerySortedSeqMetrics()