Package picard.analysis

Class CollectGcBiasMetrics

java.lang.Object
picard.cmdline.CommandLineProgram
picard.analysis.SinglePassSamProgram
picard.analysis.CollectGcBiasMetrics
@DocumentedFeature public class CollectGcBiasMetrics extends SinglePassSamProgram
Tool to collect information about GC bias in the reads in a given BAM file. Computes the number of windows (of size specified by SCAN_WINDOW_SIZE) in the genome at each GC% and counts the number of read starts in each GC bin. What is output and plotted is the "normalized coverage" in each bin - i.e. the number of reads per window normalized to the average number of reads per window across the whole genome.

  • Field Details

    • CHART_OUTPUT

      @Argument(shortName="CHART", doc="The PDF file to render the chart to.") public File CHART_OUTPUT

    • SUMMARY_OUTPUT

      @Argument(shortName="S", doc="The text file to write summary metrics to.") public File SUMMARY_OUTPUT

    • SCAN_WINDOW_SIZE

      @Argument(shortName="WINDOW_SIZE", doc="The size of the scanning windows on the reference genome that are used to bin reads.") public int SCAN_WINDOW_SIZE

    • MINIMUM_GENOME_FRACTION

      @Argument(shortName="MGF", doc="For summary metrics, exclude GC windows that include less than this fraction of the genome.") public double MINIMUM_GENOME_FRACTION

    • IS_BISULFITE_SEQUENCED

      @Argument(shortName="BS", doc="Whether the SAM or BAM file consists of bisulfite sequenced reads.") public boolean IS_BISULFITE_SEQUENCED

    • METRIC_ACCUMULATION_LEVEL

      @Argument(shortName="LEVEL", doc="The level(s) at which to accumulate metrics.") public Set<MetricAccumulationLevel> METRIC_ACCUMULATION_LEVEL

    • ALSO_IGNORE_DUPLICATES

      @Argument(shortName="ALSO_IGNORE_DUPLICATES", doc="Use to get additional results without duplicates. This option allows to gain two plots per level at the same time: one is the usual one and the other excludes duplicates.") public boolean ALSO_IGNORE_DUPLICATES

  • Constructor Details

    • CollectGcBiasMetrics

      public CollectGcBiasMetrics()

  • Method Details

    • customCommandLineValidation

      protected String[] customCommandLineValidation()
      Description copied from class: CommandLineProgram
      Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.
      Overrides:
      customCommandLineValidation in class CommandLineProgram
      Returns:
      null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.

    • setup

      protected void setup(htsjdk.samtools.SAMFileHeader header, File samFile)
      Description copied from class: SinglePassSamProgram
      Should be implemented by subclasses to do one-time initialization work.
      Specified by:
      setup in class SinglePassSamProgram

    • acceptRead

      protected void acceptRead(htsjdk.samtools.SAMRecord rec, htsjdk.samtools.reference.ReferenceSequence ref)
      Description copied from class: SinglePassSamProgram
      Should be implemented by subclasses to accept SAMRecords one at a time. If the read has a reference sequence and a reference sequence file was supplied to the program it will be passed as 'ref'. Otherwise 'ref' may be null.
      Specified by:
      acceptRead in class SinglePassSamProgram

    • finish

      protected void finish()
      Description copied from class: SinglePassSamProgram
      Should be implemented by subclasses to do one-time finalization work.
      Specified by:
      finish in class SinglePassSamProgram