Package picard.arrays

Class GtcToVcf


@DocumentedFeature public class GtcToVcf extends CommandLineProgram
Class to convert an Illumina GTC file into a VCF file.
  • Field Details

    • INPUT

      @Argument(shortName="I", doc="GTC file to be converted") public File INPUT
    • OUTPUT

      @Argument(shortName="O", doc="The output VCF file to write.") public File OUTPUT
    • EXTENDED_ILLUMINA_MANIFEST

      @Argument(shortName="MANIFEST", doc="An Extended Illumina Manifest file (csv). This is an extended version of the Illumina manifest it contains additional reference-specific fields") public File EXTENDED_ILLUMINA_MANIFEST
    • CLUSTER_FILE

      @Argument(shortName="CF", doc="An Illumina cluster file (egt)") public File CLUSTER_FILE
    • ILLUMINA_BEAD_POOL_MANIFEST_FILE

      @Argument(shortName="BPM_FILE", doc="The Illumina Bead Pool Manifest (.bpm) file") public File ILLUMINA_BEAD_POOL_MANIFEST_FILE
    • EXPECTED_GENDER

      @Argument(shortName="E_GENDER", doc="The expected gender for this sample.", optional=true) public String EXPECTED_GENDER
    • SAMPLE_ALIAS

      @Argument(doc="The sample alias") public String SAMPLE_ALIAS
    • PIPELINE_VERSION

      @Argument(doc="The version of the pipeline used to generate this VCF", optional=true) public String PIPELINE_VERSION
    • ANALYSIS_VERSION_NUMBER

      @Argument(doc="The analysis version of the data used to generate this VCF", optional=true) public Integer ANALYSIS_VERSION_NUMBER
    • GENDER_GTC

      @Argument(shortName="G_GTC", doc="An optional GTC file that was generated by calling the chip using a cluster file designed to optimize gender calling.", optional=true) public File GENDER_GTC
    • FINGERPRINT_GENOTYPES_VCF_FILE

      @Argument(shortName="FP_VCF", doc="The fingerprint VCF for this sample", optional=true) public File FINGERPRINT_GENOTYPES_VCF_FILE
    • DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS

      @Argument(doc="Causes the program to fail if it finds a case where there is a call on an assay that is flagged as \'zeroed-out\' in the Illumina cluster file.", optional=true) public boolean DO_NOT_ALLOW_CALLS_ON_ZEROED_OUT_ASSAYS
  • Constructor Details

    • GtcToVcf

      public GtcToVcf()
  • Method Details

    • requiresReference

      protected boolean requiresReference()
      Overrides:
      requiresReference in class CommandLineProgram
    • 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.
    • getGenotype

      public htsjdk.variant.variantcontext.Genotype getGenotype(String sampleName, InfiniumGTCRecord infiniumGtcRecord, IlluminaManifestRecord record, htsjdk.variant.variantcontext.Allele A, htsjdk.variant.variantcontext.Allele B)
    • formatFloatForVcf

      public static String formatFloatForVcf(float value)