Package picard.analysis

Class CollectQualityYieldMetrics.QualityYieldMetrics

  • Enclosing class:
    CollectQualityYieldMetrics
    public static class CollectQualityYieldMetrics.QualityYieldMetrics
extends htsjdk.samtools.metrics.MetricBase
    A set of metrics used to describe the general quality of a BAM file

    • Field Summary

      Fields 
      Modifier and Type Field Description
      long PF_BASES
      The total number of bases in all PF reads
      long PF_Q20_BASES
      The number of bases in PF reads that achieve quality score 20 or higher
      long PF_Q20_EQUIVALENT_YIELD
      The sum of quality scores of all bases in PF reads divided by 20
      long PF_Q30_BASES
      The number of bases in PF reads that achieve quality score 30 or higher
      long PF_READS
      The number of reads that are PF - pass filter
      long Q20_BASES
      The number of bases in all reads that achieve quality score 20 or higher
      long Q20_EQUIVALENT_YIELD
      The sum of quality scores of all bases divided by 20
      long Q30_BASES
      The number of bases in all reads that achieve quality score 30 or higher
      int READ_LENGTH
      The average read length of all the reads (will be fixed for a lane)
      long TOTAL_BASES
      The total number of bases in all reads
      long TOTAL_READS
      The total number of reads in the input file

    • Field Detail

      • TOTAL_READS

        public long TOTAL_READS
        The total number of reads in the input file

      • PF_READS

        public long PF_READS
        The number of reads that are PF - pass filter

      • READ_LENGTH

        public int READ_LENGTH
        The average read length of all the reads (will be fixed for a lane)

      • TOTAL_BASES

        public long TOTAL_BASES
        The total number of bases in all reads

      • PF_BASES

        public long PF_BASES
        The total number of bases in all PF reads

      • Q20_BASES

        public long Q20_BASES
        The number of bases in all reads that achieve quality score 20 or higher

      • PF_Q20_BASES

        public long PF_Q20_BASES
        The number of bases in PF reads that achieve quality score 20 or higher

      • Q30_BASES

        public long Q30_BASES
        The number of bases in all reads that achieve quality score 30 or higher

      • PF_Q30_BASES

        public long PF_Q30_BASES
        The number of bases in PF reads that achieve quality score 30 or higher

      • Q20_EQUIVALENT_YIELD

        public long Q20_EQUIVALENT_YIELD
        The sum of quality scores of all bases divided by 20

      • PF_Q20_EQUIVALENT_YIELD

        public long PF_Q20_EQUIVALENT_YIELD
        The sum of quality scores of all bases in PF reads divided by 20

    • Constructor Detail

      • QualityYieldMetrics

        public QualityYieldMetrics()