Template:OutBAMOutputFile
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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.
