Package picard.arrays

Class CollectArraysVariantCallingMetrics

java.lang.Object
picard.cmdline.CommandLineProgram
picard.arrays.CollectArraysVariantCallingMetrics

@DocumentedFeature public class CollectArraysVariantCallingMetrics 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 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 Details

    • CollectArraysVariantCallingMetrics

      public CollectArraysVariantCallingMetrics()
  • 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.
    • 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)