picard.analysis

Class InsertSizeMetrics

java.lang.Object

htsjdk.samtools.metrics.MetricBase

picard.metrics.MultilevelMetrics

picard.analysis.InsertSizeMetrics

public class InsertSizeMetrics
extends MultilevelMetrics

Metrics about the insert size distribution of a paired-end library, created by the CollectInsertSizeMetrics program and usually written to a file with the extension ".insert_size_metrics". In addition the insert size distribution is plotted to a file with the extension ".insert_size_Histogram.pdf".

Author:

Doug Voet (dvoet at broadinstitute dot org)

Field Summary

Fields

Modifier and Type	Field and Description
int	MAX_INSERT_SIZE The maximum measure insert size by alignment.
double	MEAN_INSERT_SIZE The mean insert size of the "core" of the distribution.
double	MEDIAN_ABSOLUTE_DEVIATION The median absolute deviation of the distribution.
double	MEDIAN_INSERT_SIZE The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.
int	MIN_INSERT_SIZE The minimum measured insert size.
htsjdk.samtools.SamPairUtil.PairOrientation	PAIR_ORIENTATION The pair orientation of the reads in this data category.
long	READ_PAIRS The total number of read pairs that were examined in the entire distribution.
double	STANDARD_DEVIATION Standard deviation of insert sizes over the "core" of the distribution.
int	WIDTH_OF_10_PERCENT The "width" of the bins, centered around the median, that encompass 10% of all read pairs.
int	WIDTH_OF_20_PERCENT The "width" of the bins, centered around the median, that encompass 20% of all read pairs.
int	WIDTH_OF_30_PERCENT The "width" of the bins, centered around the median, that encompass 30% of all read pairs.
int	WIDTH_OF_40_PERCENT The "width" of the bins, centered around the median, that encompass 40% of all read pairs.
int	WIDTH_OF_50_PERCENT The "width" of the bins, centered around the median, that encompass 50% of all read pairs.
int	WIDTH_OF_60_PERCENT The "width" of the bins, centered around the median, that encompass 60% of all read pairs.
int	WIDTH_OF_70_PERCENT The "width" of the bins, centered around the median, that encompass 70% of all read pairs.
int	WIDTH_OF_80_PERCENT The "width" of the bins, centered around the median, that encompass 80% of all read pairs.
int	WIDTH_OF_90_PERCENT The "width" of the bins, centered around the median, that encompass 90% of all read pairs.
int	WIDTH_OF_99_PERCENT The "width" of the bins, centered around the median, that encompass 100% of all read pairs.

Fields inherited from class picard.metrics.MultilevelMetrics

LIBRARY, READ_GROUP, SAMPLE

Constructor Summary

Constructors

Constructor and Description
InsertSizeMetrics()

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

MEDIAN_INSERT_SIZE

public double MEDIAN_INSERT_SIZE

The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.

MEDIAN_ABSOLUTE_DEVIATION

public double MEDIAN_ABSOLUTE_DEVIATION

The median absolute deviation of the distribution. If the distribution is essentially normal then the standard deviation can be estimated as ~1.4826 * MAD.

MIN_INSERT_SIZE

public int MIN_INSERT_SIZE

The minimum measured insert size. This is usually 1 and not very useful as it is likely artifactual.

MAX_INSERT_SIZE

public int MAX_INSERT_SIZE

The maximum measure insert size by alignment. This is usually very high representing either an artifact or possibly the presence of a structural re-arrangement.

MEAN_INSERT_SIZE

public double MEAN_INSERT_SIZE

The mean insert size of the "core" of the distribution. Artefactual outliers in the distribution often cause calculation of nonsensical mean and stdev values. To avoid this the distribution is first trimmed to a "core" distribution of +/- N median absolute deviations around the median insert size. By default N=10, but this is configurable.

STANDARD_DEVIATION

public double STANDARD_DEVIATION

Standard deviation of insert sizes over the "core" of the distribution.

READ_PAIRS

public long READ_PAIRS

The total number of read pairs that were examined in the entire distribution.

PAIR_ORIENTATION

public htsjdk.samtools.SamPairUtil.PairOrientation PAIR_ORIENTATION

The pair orientation of the reads in this data category.

WIDTH_OF_10_PERCENT

public int WIDTH_OF_10_PERCENT

The "width" of the bins, centered around the median, that encompass 10% of all read pairs.

WIDTH_OF_20_PERCENT

public int WIDTH_OF_20_PERCENT

The "width" of the bins, centered around the median, that encompass 20% of all read pairs.

WIDTH_OF_30_PERCENT

public int WIDTH_OF_30_PERCENT

The "width" of the bins, centered around the median, that encompass 30% of all read pairs.

WIDTH_OF_40_PERCENT

public int WIDTH_OF_40_PERCENT

The "width" of the bins, centered around the median, that encompass 40% of all read pairs.

WIDTH_OF_50_PERCENT

public int WIDTH_OF_50_PERCENT

The "width" of the bins, centered around the median, that encompass 50% of all read pairs.

WIDTH_OF_60_PERCENT

public int WIDTH_OF_60_PERCENT

The "width" of the bins, centered around the median, that encompass 60% of all read pairs.

WIDTH_OF_70_PERCENT

public int WIDTH_OF_70_PERCENT

The "width" of the bins, centered around the median, that encompass 70% of all read pairs. This metric divided by 2 should approximate the standard deviation when the insert size distribution is a normal distribution.

WIDTH_OF_80_PERCENT

public int WIDTH_OF_80_PERCENT

The "width" of the bins, centered around the median, that encompass 80% of all read pairs.

WIDTH_OF_90_PERCENT

public int WIDTH_OF_90_PERCENT

The "width" of the bins, centered around the median, that encompass 90% of all read pairs.

WIDTH_OF_99_PERCENT

public int WIDTH_OF_99_PERCENT

The "width" of the bins, centered around the median, that encompass 100% of all read pairs.

Constructor Detail

InsertSizeMetrics

public InsertSizeMetrics()