Package picard.vcf

Class CollectVariantCallingMetrics


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

      • INPUT

        @Argument(shortName="I",
                  doc="Input vcf file for analysis")
        public File 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 File DBSNP
      • TARGET_INTERVALS

        @Argument(shortName="TI",
                  doc="Target intervals to restrict analysis to.",
                  optional=true)
        public File 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 File 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 Detail

      • CollectVariantCallingMetrics

        public CollectVariantCallingMetrics()
    • Method Detail

      • main

        public static void main​(String[] args)
      • 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.