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 Details

    • INCLUDE_FILTERED_SHORT_NAME

      public static final String INCLUDE_FILTERED_SHORT_NAME
      See Also:
    • 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 Details

    • VcfToIntervalList

      public VcfToIntervalList()
  • 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.