Package picard.sam

Class GatherBamFiles


  • @DocumentedFeature
    public class GatherBamFiles
    extends CommandLineProgram
    Concatenate efficiently BAM files that resulted from a scattered parallel analysis.

    This tool performs a rapid "gather" or concatenation on BAM files. This is often needed in operations that have been run in parallel across genomics regions by scattering their execution across computing nodes and cores thus resulting in smaller BAM files.

    This tool does not support SAM files.

    Inputs

    A list of BAM files to combine using the INPUT argument. These files must be provided in the order that they should be concatenated.

    Output

    A single BAM file. The header is copied from the first input file.

    Usage example:

     java -jar picard.jar GatherBamFiles \
          I=input1.bam \
          I=input2.bam \
          O=gathered_files.bam
     

    Notes

    Operates via copying of the gzip blocks directly for speed but also supports generation of an MD5 on the output and indexing of the output BAM file.

    • Field Detail

      • INPUT

        @Argument(shortName="I",
                  doc="Two or more BAM files or text files containing lists of BAM files (one per line).")
        public List<File> INPUT
      • OUTPUT

        @Argument(shortName="O",
                  doc="The output BAM file to write to.")
        public File OUTPUT
    • Constructor Detail

      • GatherBamFiles

        public GatherBamFiles()
    • Method Detail

      • main

        public static void main​(String[] args)
      • 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.