Field Detail

• 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 Detail

• GtcToVcf

  public GtcToVcf()

Method Detail

• 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)