Package picard.vcf

Class VcfToIntervalList

  • @DocumentedFeature
public class VcfToIntervalList
extends CommandLineProgram
    Converts a VCF or BCF file to a Picard Interval List.

    This tool creates a Picard Interval List from a VCF or BCF. It is important that the file extension is included as the file format is determined by the file extension. Variants that were filtered can be included in the output interval list by setting INCLUDE_FILTERED to true.

    Inputs

    • A BCF or VCF input file
    • Boolean if variants that were filtered should be included in the output interval list

    Output

      A Picard Interval List

    Usage example:

         java -jar picard.jar VcfToIntervalList \
          I=input_variants.vcf \
          O=output.interval_list

    • Field Detail

      • LOG

        public static final htsjdk.samtools.util.Log LOG

      • INPUT

        @Argument(doc="The BCF or VCF input file. The file format is determined by file extension.",
          shortName="I")
public File INPUT

      • OUTPUT

        @Argument(shortName="O",
          doc="The output Picard Interval List.")
public File OUTPUT

      • INCLUDE_FILTERED

        @Argument(shortName="IF",
          doc="Include variants that were filtered in the output interval list.",
          optional=true)
public boolean INCLUDE_FILTERED

    • Constructor Detail

      • VcfToIntervalList

        public VcfToIntervalList()

    • Method Detail

      • main

        public static void main​(String[] argv)

      • 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.