Package picard.arrays

Class GtcToVcf


  • @DocumentedFeature
    public class GtcToVcf
    extends CommandLineProgram
    Class to convert a GTC file and a BPM file to a VCF file.
    • 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_NORMALIZATION_MANIFEST

        @Argument(shortName="NORM_MANIFEST",
                  doc="An Illumina bead pool manifest (a manifest containing the Illumina normalization ids) (bpm.csv)")
        public File ILLUMINA_NORMALIZATION_MANIFEST
      • 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
      • 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

      • 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)