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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 with an _# where # corresponds with the associated reference id from the BAM file.
The files all have the same base name, but with the chromosome name ".bam" or ".sam" appended.
= Usage =
./bam splitChromosome --in <inputFilename> --out <outputFileBaseName> [--noeof] [--bamout|--samout] [--params]
= Parameters =
= Parameters =
--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.
--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.
--params : print the parameter settings
--params : print the parameter settings
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{{PhoneHomeParamDesc}}
== Required Parameters ==
{{InBAMInputFile}}
=== Output File Basename (<code>--out</code>) ===
Use <code>--out</code> followed by the base output filename (no extension) to specify the SAM/BAM basename to use for the output files.
The chromosome name and the appropriate extension (sam/bam) will be appended to the specified basename.
== Optional Parameters ==
{{noeofBGZFParameter}}
= Usage =
=== Output a BAM File (<code>--bamout</code>) ===
<code>--bamout</code> indicates to output a BAM file. This flag is enabled by default.
=== Output a SAM File (<code>--samout</code>) ===
Use <code>--samout</code> to output a SAM file.
{{paramsParameter}}
{{PhoneHomeParameters}}
= Return Value =
= Return Value =
= Example Output =
= Example Output =
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<pre>
Reference ID -1 has 2 records
Reference Name: 1 has 5 records
Reference Name: 2 has 2 records
Reference ID 1 has 2 records
Reference Name: 3 has 1 records
Reference ID 2 has 1 records
Reference Name: * has 2 records
Reference ID 3 has 0 records
Number of records = 10
Number of records = 10
Returning: 0 (SUCCESS)
Returning: 0 (SUCCESS)
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