Class 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".
    • Field Summary

      Fields 
      Modifier and Type Field 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.
      double MODE_INSERT_SIZE
      The MODE insert size of all paired end reads where both ends mapped to the same chromosome.
      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_95_PERCENT
      The "width" of the bins, centered around the median, that encompass 95% 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.
    • 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.
      • 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 Detail

      • InsertSizeMetrics

        public InsertSizeMetrics()