Template:InBAMInputFile
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Jump to navigationJump to searchInput 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.