Package picard.vcf

Class MakeSitesOnlyVcf


  • @DocumentedFeature
    public class MakeSitesOnlyVcf
    extends CommandLineProgram
    Creates a VCF that contains all the site-level information for all records in the input VCF but no genotype information.

    Summary

    This tool reads a VCF/VCF.gz/BCF and removes all genotype information from it while retaining all site level information, including annotations based on genotypes (e.g. AN, AF). Output can be any supported variant format including .vcf, .vcf.gz or .bcf.

    Inputs

    • Input VCF or BCF file containing genotype and site-level information.
    • Output VCF or BCF file containing only site-level information.
    • [Optional] Names of one or more samples to include in the output VCF.

    Usage example:

         java -jar picard.jar MakeSitesOnlyVcf \
          INPUT=input_variants.vcf \
          OUTPUT=output_variants.vcf
     
    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="Input VCF or BCF containing genotype and site-level information.")
        public File INPUT
      • OUTPUT

        @Argument(shortName="O",
                  doc="Output VCF or BCF file containing only site-level information.")
        public File OUTPUT
      • SAMPLE

        @Argument(shortName="S",
                  doc="Names of one or more samples to include in the output VCF.",
                  optional=true)
        public Set<String> SAMPLE
    • Constructor Detail

      • MakeSitesOnlyVcf

        public MakeSitesOnlyVcf()
    • Method Detail

      • main

        public static void main​(String[] args)
      • 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.