Template:InBAMInputFile
From Genome Analysis Wiki
Jump to navigationJump to searchThe printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.
Input File (--in)
Use --in followed by your file name to specify the SAM/BAM input file.
The program automatically determines if your input file is SAM/BAM/uncompressed BAM without any input other than a filename from the user, unless your input file is stdin.
A - is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).
| SAM/BAM/Uncompressed BAM from file | --in yourFileName
|
| SAM from stdin | --in -
|
| BAM from stdin | --in -.bam
|
| Uncompressed BAM from stdin | --in -.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.
