Package picard.vcf

Class CollectVariantCallingMetrics

java.lang.Object
picard.cmdline.CommandLineProgram
picard.vcf.CollectVariantCallingMetrics

@DocumentedFeature public class CollectVariantCallingMetrics extends CommandLineProgram
Collects summary and per-sample metrics about variant calls in a VCF file.
  • Field Details

    • INPUT

      @Argument(shortName="I", doc="Input vcf file for analysis") public PicardHtsPath INPUT
    • OUTPUT

      @Argument(shortName="O", doc="Path (except for the file extension) of output metrics files to write.") public File OUTPUT
    • DBSNP

      @Argument(doc="Reference dbSNP file in dbSNP or VCF format.") public PicardHtsPath DBSNP
    • TARGET_INTERVALS

      @Argument(shortName="TI", doc="Target intervals to restrict analysis to.", optional=true) public PicardHtsPath TARGET_INTERVALS
    • SEQUENCE_DICTIONARY

      @Argument(shortName="SD", optional=true, doc="If present, speeds loading of dbSNP file, will look for dictionary in vcf if not present here.") public PicardHtsPath SEQUENCE_DICTIONARY
    • GVCF_INPUT

      @Argument(doc="Set to true if running on a single-sample gvcf.", optional=true) public boolean GVCF_INPUT
    • THREAD_COUNT

      @Argument public int THREAD_COUNT
  • Constructor Details

    • CollectVariantCallingMetrics

      public CollectVariantCallingMetrics()
  • Method Details

    • doWork

      protected int doWork()
      Description copied from class: CommandLineProgram
      Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.
      Specified by:
      doWork in class CommandLineProgram
      Returns:
      program exit status.