Package picard.sam

Class MergeSamFiles


@DocumentedFeature public class MergeSamFiles extends CommandLineProgram
This tool is used for combining SAM and/or BAM files from different runs or read groups into a single file, similar to the \"merge\" function of Samtools (http://www.htslib.org/doc/samtools.html).

Note that to prevent errors in downstream processing, it is critical to identify/label read groups appropriately. If different samples contain identical read group IDs, this tool will avoid collisions by modifying the read group IDs to be unique. For more information about read groups, see the GATK Dictionary entry.


Usage example:

 java -jar picard.jar MergeSamFiles \\
I=input_1.bam \\
I=input_2.bam \\
O=output_merged_files.bam

  • Field Details

    • INPUT

      @Argument(shortName="I", doc="SAM/BAM/CRAM input file", minElements=1) public List<String> INPUT
    • OUTPUT

      @Argument(shortName="O", doc="SAM/BAM/CRAM file to write merged result to") public File OUTPUT
    • SORT_ORDER

      @Argument(shortName="SO", doc="Sort order of output file", optional=true) public htsjdk.samtools.SAMFileHeader.SortOrder SORT_ORDER
    • ASSUME_SORTED

      @Argument(doc="If true, assume that the input files are in the same sort order as the requested output sort order, even if their headers say otherwise.", shortName="AS") public boolean ASSUME_SORTED
    • MERGE_SEQUENCE_DICTIONARIES

      @Argument(shortName="MSD", doc="Merge the sequence dictionaries", optional=true) public boolean MERGE_SEQUENCE_DICTIONARIES
    • USE_THREADING

      @Argument(doc="Option to create a background thread to encode, compress and write to disk the output file. The threaded version uses about 20% more CPU and decreases runtime by ~20% when writing out a compressed BAM/CRAM file.") public boolean USE_THREADING
    • COMMENT

      @Argument(doc="Comment(s) to include in the merged output file\'s header.", optional=true, shortName="CO") public List<String> COMMENT
    • INTERVALS

      @Argument(shortName="RGN", doc="An interval list file that contains the locations of the positions to merge. Assume sam are sorted and indexed. The resulting file will contain alignments that may overlap with genomic regions outside the requested region. Unmapped reads are discarded.", optional=true) public File INTERVALS
  • Constructor Details

    • MergeSamFiles

      public MergeSamFiles()
  • Method Details

    • doWork

      protected int doWork()
      Combines multiple SAM/BAM/CRAM files into one.
      Specified by:
      doWork in class CommandLineProgram
      Returns:
      program exit status.
    • customCommandLineValidation

      protected String[] customCommandLineValidation()
      Description copied from class: CommandLineProgram
      Put any custom command-line validation in an override of this method. clp is initialized at this point and can be used to print usage and access argv. Any options set by command-line parser can be validated.
      Overrides:
      customCommandLineValidation in class CommandLineProgram
      Returns:
      null if command line is valid. If command line is invalid, returns an array of error message to be written to the appropriate place.