Difference between revisions of "Template:OutBAMOutputFile"
From Genome Analysis Wiki
Jump to navigationJump to search (--out BAM Output File) |
|||
Line 1: | Line 1: | ||
− | == output File (<code>--out</code>) == | + | {{{hdr|==}}} output File (<code>--out</code>) {{{hdr|==}}} |
Use <code>--out</code> followed by your file name to specify the SAM/BAM output file. | Use <code>--out</code> followed by your file name to specify the SAM/BAM output file. |
Revision as of 17:26, 3 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.