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== SplitBam ==
= Overview of the <code>splitBam</code> function of <code>bamUtil</code> =
The <code>splitBam</code> option on the [[bamUtil]] executable split a BAM file into multiple BAM files based on ReadGroup according to the following details.
# Creates multiple output files named [outprefix].[RGID].bam, for each ReadGroup ID (RGID) existing in the bam file
# Creates multiple output files named [outprefix].[RGID].bam, for each ReadGroup ID (RGID) existing in the bam file
# Headers are a copy of the original file, removing @RG and @PG headers where IDs match with the other ReadGroup IDs.
# Headers are a copy of the original file, removing @RG and @PG headers where IDs match with the other ReadGroup IDs.
# Copy each of the original file's BAM record to one of the output file where the ReadGroup ID matches
# Copy each of the original file's BAM record to one of the output file where the ReadGroup ID matches
= Usage =
./bam splitBam [-v] -i <inputBAMFile> -o <outPrefix> [-L logFile]
= Parameters =
<pre>
<pre>
Required arguments:
-i/--in [inputBAMFile] : Original BAM file containing readGroup info
-o/--out [outPrefix] : prefix of output bam files of [outprefix].[RGID].bam
Optional arguments:
-L/--log [logFile] : log file name. default is listFile.log
-v/--verbose : turn on verbose mode
-n/--noeof : turn off the check for an EOF block at the end of a bam file
</pre>
</pre>
{{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 BAM basename to use for the output files.
The read group name and <code>.bam</code> will be appended to the specified basename.
== Optional Parameters ==
=== Specify Log Filename (<code>--log</code>) ===
Use <code>--log</code> followed by the log filename to specify the log filename. Default is the output file basename with a <code>.log</code> extension
=== Verbose (<code>--verbose</code>) ===
Use <code>--verbose</code> to turn on verbose mode.
{{noeofBGZFParameter}}
{{PhoneHomeParameters}}
= Return Value =
* 0: Success.
* non-0: Failure.
[[Category:BamUtil|splitBam]]
[[Category:BAM Software]]
[[Category:Software]]
[[Category:Software]]
