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{{PhoneHomeParamDesc}}
{{PhoneHomeParamDesc}}
== Required Parameters ==
{{InBAMInputFile}}
{{InBAMInputFile}}
== Output File Basename (<code>--out</code>) ==
=== 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.
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.
The chromosome name and the appropriate extension (sam/bam) will be appended to the specified basename.
== Optional Parameters ==
{{noeofBGZFParameter}}
{{noeofBGZFParameter}}
== Output a BAM File (<code>--bamout</code>) ==
=== Output a BAM File (<code>--bamout</code>) ===
<code>--bamout</code> indicates to output a BAM file. This flag is enabled by default.
<code>--bamout</code> indicates to output a BAM file. This flag is enabled by default.
== Output a SAM File (<code>--samout</code>) ==
=== Output a SAM File (<code>--samout</code>) ===
Use <code>--samout</code> to output a SAM file.
Use <code>--samout</code> to output a SAM file.
