Difference between revisions of "BamUtil: splitChromosome"
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The <code>splitChromosome</code> option on the [[bamUtil]] executable splits an indexed BAM file into multiple files based on the Chromosome (Reference Name). | 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 | + | The files all have the same base name, but with the chromosome name ".bam" or ".sam" appended. |
= Parameters = | = Parameters = | ||
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--in : the BAM file to be split | --in : the BAM file to be split | ||
--out : the base filename for the SAM/BAM files to write into. Does not include the extension. | --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: | Optional Parameters: | ||
--noeof : do not expect an EOF block on a bam file. | --noeof : do not expect an EOF block on a bam file. | ||
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--bamout : write the output files in BAM format (default). | --bamout : write the output files in BAM format (default). | ||
--samout : write the output files in SAM format. | --samout : write the output files in SAM format. | ||
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= Usage = | = Usage = | ||
| − | ./bam splitChromosome --in <inputFilename> --out <outputFileBaseName> | + | ./bam splitChromosome --in <inputFilename> --out <outputFileBaseName> [--noeof] [--bamout|--samout] [--params] |
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= Example Output = | = Example Output = | ||
<pre> | <pre> | ||
| − | Reference | + | Reference Name: 1 has 5 records |
| − | + | Reference Name: 2 has 2 records | |
| − | Reference | + | Reference Name: 3 has 1 records |
| − | Reference | + | Reference Name: * has 2 records |
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Number of records = 10 | Number of records = 10 | ||
Returning: 0 (SUCCESS) | Returning: 0 (SUCCESS) | ||
</pre> | </pre> | ||
Revision as of 16:07, 16 July 2012
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)
