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, 11:42, 3 April 2012
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− | == Trim BAM == | + | = Overview of the <code>trimBam</code> function of <code>bamUtil</code> = |
− | The <code>trimBam</code> program is released as part of the StatGen Library & Tools download. | + | The <code>trimBam</code> option on the [[bamUtil]] executable trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’. |
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− | <code>trimBam</code> trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.
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| + | = Usage = |
| + | ./bam trimBam [inFile] [outFile] [num-bases-to-trim-on-each-side] |
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− | === Parameters ===
| + | |
| + | = Parameters = |
| <pre> | | <pre> |
| Required Parameters: | | Required Parameters: |
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| num-bases-to-trim-on-each-side : the number of bases/qualities to trim from each side | | num-bases-to-trim-on-each-side : the number of bases/qualities to trim from each side |
| </pre> | | </pre> |
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− | === Usage ===
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− | trimBam [inFile] [outFile] [num-bases-to-trim-on-each-side]
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− | === Return Value ===
| + | = Return Value = |
| Returns the SamStatus for the reads/writes. 0 on success. | | Returns the SamStatus for the reads/writes. 0 on success. |
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− | === Example Output ===
| + | = Example Output = |
| <pre> | | <pre> |
| Arguments in effect: | | Arguments in effect: |
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| </pre> | | </pre> |
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| + | [[Category:BamUtil|trimBam]] |
| + | [[Category:BAM Software]] |
| [[Category:Software]] | | [[Category:Software]] |
− | [[Category:StatGen Download]]
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− | [[Category:BAM Software]]
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