Class RrbsSummaryMetrics

java.lang.Object
htsjdk.samtools.metrics.MetricBase
picard.metrics.MultilevelMetrics
picard.analysis.RrbsSummaryMetrics

@DocumentedFeature(groupName="Metrics", summary="Metrics") public final class RrbsSummaryMetrics extends MultilevelMetrics
Holds summary statistics from RRBS processing QC
  • Field Details

    • READS_ALIGNED

      public Integer READS_ALIGNED
      Number of mapped reads processed
    • NON_CPG_BASES

      public Integer NON_CPG_BASES
      Number of times a non-CpG cytosine was encountered
    • NON_CPG_CONVERTED_BASES

      public Integer NON_CPG_CONVERTED_BASES
      Number of times a non-CpG cytosine was converted (C->T for +, G->A for -)
    • PCT_NON_CPG_BASES_CONVERTED

      public Double PCT_NON_CPG_BASES_CONVERTED
      NON_CPG_CONVERTED_BASES / NON_CPG_BASES (fraction)
    • CPG_BASES_SEEN

      public Integer CPG_BASES_SEEN
      Number of CpG sites encountered
    • CPG_BASES_CONVERTED

      public Integer CPG_BASES_CONVERTED
      Number of CpG sites that were converted (TG for +, CA for -)
    • PCT_CPG_BASES_CONVERTED

      public Double PCT_CPG_BASES_CONVERTED
      CPG_BASES_CONVERTED / CPG_BASES_SEEN (fraction)
    • MEAN_CPG_COVERAGE

      public Double MEAN_CPG_COVERAGE
      Mean coverage of CpG sites
    • MEDIAN_CPG_COVERAGE

      public Integer MEDIAN_CPG_COVERAGE
      Median coverage of CpG sites
    • READS_WITH_NO_CPG

      public Integer READS_WITH_NO_CPG
      Number of reads discarded for having no CpG sites
    • READS_IGNORED_SHORT

      public Integer READS_IGNORED_SHORT
      Number of reads discarded due to being too short
    • READS_IGNORED_MISMATCHES

      public Integer READS_IGNORED_MISMATCHES
      Number of reads discarded for exceeding the mismatch threshold
  • Constructor Details

    • RrbsSummaryMetrics

      public RrbsSummaryMetrics()