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Revision as of 13:32, 2 September 2011
, 13:32, 2 September 2011Add splitChromosome
[[Category:BamUtil|splitChromosome]]
[[Category:BAM Software]]
[[Category:Software]]
= Overview of the <code>splitChromosome</code> function of <code>bamUtil</code> =
The <code>splitChromosome</code> 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 an _# where # corresponds with the associated reference id from the BAM file.
= Parameters =
<pre>
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.
_N will be appended to the basename where N indicates the Chromosome.
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--bamIndex : the path/name of the bam index file
(if not specified, uses the --in value + ".bai")
--bamout : write the output files in BAM format (default).
--samout : write the output files in SAM format.
--params : print the parameter settings
</pre>
= Usage =
./bam splitChromosome --in <inputFilename> --out <outputFileBaseName> [--bamIndex <bamIndexFile>] [--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 =
<pre>
Reference ID -1 has 2 records
Reference ID 0 has 5 records
Reference ID 1 has 2 records
Reference ID 2 has 1 records
Reference ID 3 has 0 records
Reference ID 4 has 0 records
Reference ID 5 has 0 records
Reference ID 6 has 0 records
Reference ID 7 has 0 records
Reference ID 8 has 0 records
Reference ID 9 has 0 records
Reference ID 10 has 0 records
Reference ID 11 has 0 records
Reference ID 12 has 0 records
Reference ID 13 has 0 records
Reference ID 14 has 0 records
Reference ID 15 has 0 records
Reference ID 16 has 0 records
Reference ID 17 has 0 records
Reference ID 18 has 0 records
Reference ID 19 has 0 records
Reference ID 20 has 0 records
Reference ID 21 has 0 records
Reference ID 22 has 0 records
Number of records = 10
Returning: 0 (SUCCESS)
</pre>
[[Category:BAM Software]]
[[Category:Software]]
= Overview of the <code>splitChromosome</code> function of <code>bamUtil</code> =
The <code>splitChromosome</code> 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 an _# where # corresponds with the associated reference id from the BAM file.
= Parameters =
<pre>
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.
_N will be appended to the basename where N indicates the Chromosome.
Optional Parameters:
--noeof : do not expect an EOF block on a bam file.
--bamIndex : the path/name of the bam index file
(if not specified, uses the --in value + ".bai")
--bamout : write the output files in BAM format (default).
--samout : write the output files in SAM format.
--params : print the parameter settings
</pre>
= Usage =
./bam splitChromosome --in <inputFilename> --out <outputFileBaseName> [--bamIndex <bamIndexFile>] [--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 =
<pre>
Reference ID -1 has 2 records
Reference ID 0 has 5 records
Reference ID 1 has 2 records
Reference ID 2 has 1 records
Reference ID 3 has 0 records
Reference ID 4 has 0 records
Reference ID 5 has 0 records
Reference ID 6 has 0 records
Reference ID 7 has 0 records
Reference ID 8 has 0 records
Reference ID 9 has 0 records
Reference ID 10 has 0 records
Reference ID 11 has 0 records
Reference ID 12 has 0 records
Reference ID 13 has 0 records
Reference ID 14 has 0 records
Reference ID 15 has 0 records
Reference ID 16 has 0 records
Reference ID 17 has 0 records
Reference ID 18 has 0 records
Reference ID 19 has 0 records
Reference ID 20 has 0 records
Reference ID 21 has 0 records
Reference ID 22 has 0 records
Number of records = 10
Returning: 0 (SUCCESS)
</pre>
