Package picard.arrays

Class CollectArraysVariantCallingMetrics


  • @DocumentedFeature
    public class CollectArraysVariantCallingMetrics
    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
      • CALL_RATE_PF_THRESHOLD

        @Argument(doc="The Call Rate Threshold for an autocall pass (if the observed call rate is > this value, the sample is considered to be passing)",
                  optional=true)
        public static Double CALL_RATE_PF_THRESHOLD
      • DBSNP

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

        @Argument(doc="Split this task over multiple threads.  If NUM_PROCESSORS = 0, number of cores is automatically set to the number of cores available on the machine. If NUM_PROCESSORS < 0 then the number of cores used will be the number available on the machine less NUM_PROCESSORS.")
        public int NUM_PROCESSORS
    • Constructor Detail

      • CollectArraysVariantCallingMetrics

        public CollectArraysVariantCallingMetrics()
    • Method Detail

      • 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.
      • 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.
      • getSexConcordance

        public static boolean getSexConcordance​(String reportedSexString,
                                                String fingerprintSexString,
                                                String autocallSexString)