Package picard.vcf

Class MakeVcfSampleNameMap

java.lang.Object
picard.cmdline.CommandLineProgram
picard.vcf.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 Details

    • 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 Details

    • MakeVcfSampleNameMap

      public MakeVcfSampleNameMap()
  • 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.