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

      • VARIANT_ID_METHOD

        @Argument(doc="Controls the naming of the resulting intervals. When set to CONCAT_ALL (the default), each resulting interval will be named the concatenation of the variant ID fields (if present), or \'interval-<number>\' (if not) with a pipe \'|\' separator. If set to USE_FIRST, only the first name will be used.")
public static VcfToIntervalList.VARIANT_ID_TYPES VARIANT_ID_METHOD

      • 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

      • 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.