From Genome Analysis Wiki
Jump to navigationJump to search
1,664 bytes removed
, 16:58, 6 January 2014
| Line 33: |
Line 33: |
| | | | |
| | == Required Parameters== | | == Required Parameters== |
| − | === Input File (1st argument) ===
| |
| | | | |
| − | The first argument is the name of the SAM/BAM input file.
| + | {{InBAMInputFile|noParam=1st}} |
| | + | {{OutBAMOutputFile|noParam=2nd}} |
| | | | |
| − | 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 <code>-</code> is used to indicate to read from stdin and the extension is used to determine the file type (no extension indicates SAM).
| |
| − |
| |
| − | {|border="1" cellspacing="0" cellpadding="2"
| |
| − | |SAM/BAM/Uncompressed BAM from file
| |
| − | | <code>yourFileName</code>
| |
| − | |-
| |
| − | |SAM from stdin
| |
| − | | <code>-</code>
| |
| − | |-
| |
| − | |BAM from stdin
| |
| − | | <code>-.bam</code>
| |
| − | |-
| |
| − | |Uncompressed BAM from stdin
| |
| − | | <code>-.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.
| |
| − |
| |
| − | === output File (2nd argument) ===
| |
| − |
| |
| − | The second argument is the name of 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).
| |
| − |
| |
| − | {|border="1" cellspacing="0" cellpadding="2"
| |
| − | |SAM to file
| |
| − | | <code>yourFileName.sam</code>
| |
| − | |-
| |
| − | |BAM to file
| |
| − | | <code>yourFileName.bam</code>
| |
| − | |-
| |
| − | |Uncompressed BAM to file
| |
| − | | <code>yourFileName.ubam</code>
| |
| − | |-
| |
| − | |SAM to stdout
| |
| − | | <code>-</code>
| |
| − | |-
| |
| − | |BAM to stdout
| |
| − | | <code>-.bam</code>
| |
| − | |-
| |
| − | |Uncompressed BAM to stdout
| |
| − | | <code>-.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.
| |
| | ==Optional parameters== | | ==Optional parameters== |
| | === Number of Bases to Trim from Each End (3rd argument) === | | === Number of Bases to Trim from Each End (3rd argument) === |
