View source for Template:OutBAMOutputFile

{{{hdr|===}}} Output File ({{#if: {{{noParam|}}} | {{{noParam}}} argument|<code>{{{param|--out}}}</code>}}) {{{hdr|===}}}

{{#if: {{{noParam|}}} | The {{{noParam}}} argument is the name of the output SAM/BAM file. |
Use <code>{{{param|--out}}}</code> followed by your file name to specify the SAM/BAM output file.}}

The file extension is used to determine whether to write SAM/BAM/uncompressed BAM.  A <code>-</code> is used to indicate stdout and the extension for file type (no extension is SAM).

{|border="1" cellspacing="0" cellpadding="2"
|SAM to file
| <code>{{#if: {{{noParam|}}} | |--out}} yourFileName.sam</code>
|-
|BAM to file
| <code>{{#if: {{{noParam|}}} | |--out}} yourFileName.bam</code>
|-
|Uncompressed BAM to file
| <code>{{#if: {{{noParam|}}} | |--out}} yourFileName.ubam</code>
|-
|SAM to stdout
| <code>{{#if: {{{noParam|}}} | |--out}} -</code>
|-
|BAM to stdout
| <code>{{#if: {{{noParam|}}} | |--out}} -.bam</code>
|-
|Uncompressed BAM to stdout
| <code>{{#if: {{{noParam|}}} | |--out}} -.ubam</code>
|}


Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file).  This matches the <code>samtools</code> implementation so pipes between our tools and <code>samtools</code> are supported.