Package picard.analysis
Class InsertSizeMetrics
java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.metrics.MultilevelMetrics
picard.analysis.InsertSizeMetrics
@DocumentedFeature(groupName="Metrics",
summary="Metrics")
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".
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Field Summary
FieldsModifier and TypeFieldDescriptionint
The maximum measure insert size by alignment.double
The mean insert size of the "core" of the distribution.double
The median absolute deviation of the distribution.double
The MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome.int
The minimum measured insert size.double
The MODE insert size of all paired end reads where both ends mapped to the same chromosome.htsjdk.samtools.SamPairUtil.PairOrientation
The pair orientation of the reads in this data category.long
The total number of read pairs that were examined in the entire distribution.double
Standard deviation of insert sizes over the "core" of the distribution.int
The "width" of the bins, centered around the median, that encompass 10% of all read pairs.int
The "width" of the bins, centered around the median, that encompass 20% of all read pairs.int
The "width" of the bins, centered around the median, that encompass 30% of all read pairs.int
The "width" of the bins, centered around the median, that encompass 40% of all read pairs.int
The "width" of the bins, centered around the median, that encompass 50% of all read pairs.int
The "width" of the bins, centered around the median, that encompass 60% of all read pairs.int
The "width" of the bins, centered around the median, that encompass 70% of all read pairs.int
The "width" of the bins, centered around the median, that encompass 80% of all read pairs.int
The "width" of the bins, centered around the median, that encompass 90% of all read pairs.int
The "width" of the bins, centered around the median, that encompass 95% of all read pairs.int
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
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Constructor Summary
Constructors -
Method Summary
Methods inherited from class htsjdk.samtools.metrics.MetricBase
equals, hashCode, toString
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Field Details
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MEDIAN_INSERT_SIZE
public double MEDIAN_INSERT_SIZEThe MEDIAN insert size of all paired end reads where both ends mapped to the same chromosome. -
MODE_INSERT_SIZE
public double MODE_INSERT_SIZEThe MODE insert size of all paired end reads where both ends mapped to the same chromosome. -
MEDIAN_ABSOLUTE_DEVIATION
public double MEDIAN_ABSOLUTE_DEVIATIONThe 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_SIZEThe minimum measured insert size. This is usually 1 and not very useful as it is likely artifactual. -
MAX_INSERT_SIZE
public int MAX_INSERT_SIZEThe 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_SIZEThe 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_DEVIATIONStandard deviation of insert sizes over the "core" of the distribution. -
READ_PAIRS
public long READ_PAIRSThe total number of read pairs that were examined in the entire distribution. -
PAIR_ORIENTATION
public htsjdk.samtools.SamPairUtil.PairOrientation PAIR_ORIENTATIONThe pair orientation of the reads in this data category. -
WIDTH_OF_10_PERCENT
public int WIDTH_OF_10_PERCENTThe "width" of the bins, centered around the median, that encompass 10% of all read pairs. -
WIDTH_OF_20_PERCENT
public int WIDTH_OF_20_PERCENTThe "width" of the bins, centered around the median, that encompass 20% of all read pairs. -
WIDTH_OF_30_PERCENT
public int WIDTH_OF_30_PERCENTThe "width" of the bins, centered around the median, that encompass 30% of all read pairs. -
WIDTH_OF_40_PERCENT
public int WIDTH_OF_40_PERCENTThe "width" of the bins, centered around the median, that encompass 40% of all read pairs. -
WIDTH_OF_50_PERCENT
public int WIDTH_OF_50_PERCENTThe "width" of the bins, centered around the median, that encompass 50% of all read pairs. -
WIDTH_OF_60_PERCENT
public int WIDTH_OF_60_PERCENTThe "width" of the bins, centered around the median, that encompass 60% of all read pairs. -
WIDTH_OF_70_PERCENT
public int WIDTH_OF_70_PERCENTThe "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_PERCENTThe "width" of the bins, centered around the median, that encompass 80% of all read pairs. -
WIDTH_OF_90_PERCENT
public int WIDTH_OF_90_PERCENTThe "width" of the bins, centered around the median, that encompass 90% of all read pairs. -
WIDTH_OF_95_PERCENT
public int WIDTH_OF_95_PERCENTThe "width" of the bins, centered around the median, that encompass 95% of all read pairs. -
WIDTH_OF_99_PERCENT
public int WIDTH_OF_99_PERCENTThe "width" of the bins, centered around the median, that encompass 100% of all read pairs.
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Constructor Details
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InsertSizeMetrics
public InsertSizeMetrics()
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