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 Details

    • INPUT

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

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

    • GatherBamFiles

      public GatherBamFiles()
  • 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.