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1,664 bytes removed
, 16:58, 6 January 2014
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| == Required Parameters== | | == Required Parameters== |
− | === Input File (1st argument) ===
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− | The first argument is the name of the SAM/BAM input file.
| + | {{InBAMInputFile|noParam=1st}} |
| + | {{OutBAMOutputFile|noParam=2nd}} |
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− | 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.
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− |
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− | 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).
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− |
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− | {|border="1" cellspacing="0" cellpadding="2"
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− | |SAM/BAM/Uncompressed BAM from file
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− | | <code>yourFileName</code>
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− | |-
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− | |SAM from stdin
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− | | <code>-</code>
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− | |-
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− | |BAM from stdin
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− | | <code>-.bam</code>
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− | |-
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− | |Uncompressed BAM from stdin
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− | | <code>-.ubam</code>
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− | |}
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− | 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.
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− |
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− | === output File (2nd argument) ===
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− |
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− | The second argument is the name of the SAM/BAM output file.
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− |
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− | 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).
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− |
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− | {|border="1" cellspacing="0" cellpadding="2"
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− | |SAM to file
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− | | <code>yourFileName.sam</code>
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− | |-
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− | |BAM to file
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− | | <code>yourFileName.bam</code>
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− | |-
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− | |Uncompressed BAM to file
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− | | <code>yourFileName.ubam</code>
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− | |-
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− | |SAM to stdout
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− | | <code>-</code>
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− | |-
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− | |BAM to stdout
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− | | <code>-.bam</code>
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− | |-
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− | |Uncompressed BAM to stdout
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− | | <code>-.ubam</code>
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− | |}
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− |
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− |
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− | 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.
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| ==Optional parameters== | | ==Optional parameters== |
| === Number of Bases to Trim from Each End (3rd argument) === | | === Number of Bases to Trim from Each End (3rd argument) === |