Package picard.vcf

Class MakeVcfSampleNameMap


  • public class MakeVcfSampleNameMap
    extends CommandLineProgram
    Creates a TSV from sample name to VCF/GVCF path, with one line per input.

    Summary

    Creates a TSV from sample name to VCF/GVCF path, with one line per input. Input VCF/GVCFs must contain a header describing exactly one sample.

    Usage example:

         java -jar picard.jar MakeVcfSampleNameMap \
          INPUT=sample1.vcf.gz \
          INPUT=sample2.vcf.gz \
          OUTPUT=cohort.sample_map
     
    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="One or more input VCFs to extract sample names from.",
                  minElements=1)
        public List<String> INPUT
      • OUTPUT

        @Argument(shortName="O",
                  doc="Output file to write the sample-name map to.")
        public File OUTPUT
    • Constructor Detail

      • MakeVcfSampleNameMap

        public MakeVcfSampleNameMap()
    • 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.