BamUtil: splitChromosome

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Revision as of 17:07, 16 July 2012 by Mktrost (talk | contribs) (Updated to actually split all chromsomes)
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Overview of the splitChromosome function of bamUtil

The splitChromosome option on the bamUtil executable splits an indexed BAM file into multiple files based on the Chromosome (Reference Name).

The files all have the same base name, but with the chromosome name ".bam" or ".sam" appended.

Parameters

    Required Parameters:
        --in       : the BAM file to be split
        --out      : the base filename for the SAM/BAM files to write into.  Does not include the extension.
                     CHROM.bam or CHROM.sam will be appended to the basename where CHROM is the chromosome name.
    Optional Parameters:
        --noeof  : do not expect an EOF block on a bam file.
        --bamout : write the output files in BAM format (default).
        --samout : write the output files in SAM format.
        --params : print the parameter settings

Usage

./bam splitChromosome --in <inputFilename>  --out <outputFileBaseName> [--noeof] [--bamout|--samout] [--params]


Return Value

  • 0: all records are successfully read and written.
  • non-0: at least one record was not successfully read or written.

Example Output

Reference Name: 1 has 5 records
Reference Name: 2 has 2 records
Reference Name: 3 has 1 records
Reference Name: * has 2 records
Number of records = 10
Returning: 0 (SUCCESS)