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".
  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    int
    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
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • 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 Details

    • 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.
    • MODE_INSERT_SIZE

      public double MODE_INSERT_SIZE
      The MODE 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_95_PERCENT

      public int WIDTH_OF_95_PERCENT
      The "width" of the bins, centered around the median, that encompass 95% 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 Details

    • InsertSizeMetrics

      public InsertSizeMetrics()