Template:OutBAMOutputFile: Difference between revisions
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{{{hdr|==}}} | {{{hdr|===}}} Output File ({{#if: {{{noParam|}}} | {{{noParam}}} argument|<code>{{{param|--out}}}</code>}}) {{{hdr|===}}} | ||
Use <code>--out</code> followed by your file name to specify the SAM/BAM output file. | {{#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). | 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). | ||
| Line 7: | Line 8: | ||
{|border="1" cellspacing="0" cellpadding="2" | {|border="1" cellspacing="0" cellpadding="2" | ||
|SAM to file | |SAM to file | ||
| <code>--out yourFileName.sam</code> | | <code>{{#if: {{{noParam|}}} | |--out}} yourFileName.sam</code> | ||
|- | |- | ||
|BAM to file | |BAM to file | ||
| <code>--out yourFileName.bam</code> | | <code>{{#if: {{{noParam|}}} | |--out}} yourFileName.bam</code> | ||
|- | |- | ||
|Uncompressed BAM to file | |Uncompressed BAM to file | ||
| <code>--out yourFileName.ubam</code> | | <code>{{#if: {{{noParam|}}} | |--out}} yourFileName.ubam</code> | ||
|- | |- | ||
|SAM to stdout | |SAM to stdout | ||
| <code>--out -</code> | | <code>{{#if: {{{noParam|}}} | |--out}} -</code> | ||
|- | |- | ||
|BAM to stdout | |BAM to stdout | ||
| <code>--out -.bam</code> | | <code>{{#if: {{{noParam|}}} | |--out}} -.bam</code> | ||
|- | |- | ||
|Uncompressed BAM to stdout | |Uncompressed BAM to stdout | ||
| <code>--out -.ubam</code> | | <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. | 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. | ||
Latest revision as of 16:56, 6 January 2014
Output File (--out)
Use --out 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 - is used to indicate stdout and the extension for file type (no extension is SAM).
| SAM to file | --out yourFileName.sam
|
| BAM to file | --out yourFileName.bam
|
| Uncompressed BAM to file | --out yourFileName.ubam
|
| SAM to stdout | --out -
|
| BAM to stdout | --out -.bam
|
| Uncompressed BAM to stdout | --out -.ubam
|
Note: Uncompressed BAM is compressed using compression level-0 (so it is not an entirely uncompressed file). This matches the samtools implementation so pipes between our tools and samtools are supported.
