Package picard.vcf

Class RenameSampleInVcf


@DocumentedFeature public class RenameSampleInVcf extends CommandLineProgram
Renames a sample within a VCF or BCF.

Summary

This tool enables the user to rename a sample in either a VCF or BCF file. It is intended to change the name of a sample in a VCF prior to merging with VCF files in which one or more samples have similar names. Note that the input VCF file must be single-sample VCF and that the NEW_SAMPLE_NAME argument is required.

Inputs

  • Input single-sample VCF or BCF file.
  • Output single-sample VCF or BCF file.
  • New name to give sample in output VCF.
  • [Optional] Existing name of sample in VCF; if provided, asserts that that is the name of the extant sample name.

Usage example:

     java -jar picard.jar RenameSampleInVcf \
     INPUT=input_variants.vcf \
     OUTPUT=output_variants.vcf \
     NEW_SAMPLE_NAME=sample
 

Notes

The input VCF (or BCF) must be single-sample.
  • Field Details

    • INPUT

      @Argument(shortName="I", doc="Input single sample VCF or BCF file.") public File INPUT
    • OUTPUT

      @Argument(shortName="O", doc="Output single sample VCF.") public File OUTPUT
    • OLD_SAMPLE_NAME

      @Argument(doc="Existing name of sample in VCF; if provided, asserts that that is the name of the extant sample name", optional=true) public String OLD_SAMPLE_NAME
    • NEW_SAMPLE_NAME

      @Argument(doc="New name to give sample in output VCF.") public String NEW_SAMPLE_NAME
  • Constructor Details

    • RenameSampleInVcf

      public RenameSampleInVcf()
  • 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.