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= Usage=
= Usage=
<pre>
<pre>
mergeBam [-v] [--log logFile] [--ignorePI] --list <listFile> --out <outFile>
</pre>
</pre>
* (Required fields)
* (Required fields)
Optional parameters :
Optional parameters :
--ignorePI/-I : Ignore the RG PI field when comparing headers
--log/-L : Log file
--log/-L : Log file
--verbose/-v : Turn on verbose mode
--verbose/-v : Turn on verbose mode
</pre>
</pre>
== Required Parameters==
=== Input Files (<code>--in</code>, <code>--list</code>) ===
Use multiple <code>--in</code> parameters each followed by an input file name to specify the SAM/BAM input files (more than one <code>--in</code> must be specified).
Alternatively, a RGAList file can be specified using <code>--list</code>. The specified file contains a header row with a tab delimited list of the included columns followed by a row for each BAM file with a tab-delimited list of the values for each column.
The possible header column name are (* indicates required fields):
* BAM* : Input BAM file name to be merged
* ID* : Unique read group identifier
* SM* : Sample name
* LB : Library name
* DS : Description
* PU : Platform unit
* PI : Predicted median insert size
* CN : Name of sequencing center producing the read
* DT : Date the rn was produced
* PL : Platform/technology used to produce the read
The program automatically determines if your input files are SAM/BAM/uncompressed BAM.
{{OutBAMOutputFile}}
== Optional Parameters ==
=== Specify Log Filename (<code>--ignorePI</code> or <code>-I</code>) ===
Use <code>--ignorePI</code> to ignore the RG PI field when comparing headers. The field from the first header will be used in the output file.
This parameter was added in version 1.0.10.
=== 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.
{{PhoneHomeParameters}}
= Return Value =
Returns 0 on success, non-0 on failure.
[[Category:BamUtil|mergeBam]]
[[Category:BamUtil|mergeBam]]
[[Category:BAM Software]]
[[Category:BAM Software]]
[[Category:Software]]
[[Category:Software]]
