Package picard.util

Class ScatterIntervalsByNs

java.lang.Object
picard.cmdline.CommandLineProgram
picard.util.ScatterIntervalsByNs

@DocumentedFeature public class ScatterIntervalsByNs extends CommandLineProgram
A Tool for breaking up a reference into intervals of alternating regions of N and ACGT bases.

Summary

Used for creating a broken-up interval list that can be used for scattering a variant-calling pipeline in a way that will not cause problems at the edges of the intervals. By using large enough N blocks (so that the tools will not be able to anchor on both sides) we can be assured that the results of scattering and gathering the variants with the resulting interval list will be the same as calling with one large region.

Input

  • A reference file to use for creating the intervals
  • Which type of intervals to emit in the output (Ns only, ACGT only or both).
  • An integer indicating the largest number of Ns in a contiguous block that will be "tolerated" and not converted into an N block.

  • Output


    An interval list (with a SAM header) where the names of the intervals are labeled (either N-block or ACGT-block) to indicate what type of block they define.

    Usage example

    Create an interval list of intervals that do not contain any N blocks for use with haplotype caller on short reads

     java -jar picard.jar ScatterIntervalsByNs \
           R=reference_sequence.fasta \
           OT=BOTH \
           O=output.interval_list
     
    • Field Details

      • OUTPUT

        @Argument(shortName="O", doc="Output file for interval list.") public File OUTPUT
      • OUTPUT_TYPE

        @Argument(shortName="OT", doc="Type of intervals to output.", optional=true) public picard.util.ScatterIntervalsByNs.OutputType OUTPUT_TYPE
      • MAX_TO_MERGE

        @Argument(shortName="N", doc="Maximal number of contiguous N bases to tolerate, thereby continuing the current ACGT interval.", optional=true) public int MAX_TO_MERGE
    • Constructor Details

      • ScatterIntervalsByNs

        public ScatterIntervalsByNs()
    • Method Details