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, 18:26, 3 January 2014
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| = Overview of the <code>findCigars</code> function of <code>bamUtil</code> = | | = Overview of the <code>findCigars</code> function of <code>bamUtil</code> = |
| The <code>findCigars</code> option on the [[bamUtil]] executable outputs just the reads that contain any of the specified CIGAR operations. | | The <code>findCigars</code> option on the [[bamUtil]] executable outputs just the reads that contain any of the specified CIGAR operations. |
| + | |
| + | = Usage = |
| + | ./bam findCigars --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--cinsert] [--cdel] [--cpad] [--cskip] [--chardClip] [--csoftClip] [--nonM] [--noeof] [--params] |
| | | |
| = Parameters = | | = Parameters = |
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| --params : print the parameter settings | | --params : print the parameter settings |
| </pre> | | </pre> |
| + | {{PhoneHomeParamDesc}} |
| + | |
| + | == Required Parameters == |
| + | {{InBAMInputFile}} |
| + | {{OutBAMOutputFile}} |
| + | |
| + | == CIGAR Selection Parameters (<code>--cinsert</code>, <code>--cdel</code>, <code>--cpad</code>, <code>--cskip</code>, <code>--chardClip</code>, <code>--csoftClip</code>, <code>--nonM</code>) == |
| + | Use these parameters to select which reads to keep based on the cigar. By default, none of these options are on, so no reads would be kept. |
| + | |
| + | Keep any read with any of the specified cigar operators (multiple can be specified and a read that has any of them will be kept): |
| + | * --cinsert : insertion |
| + | * --cdel : deletion |
| + | * --cpad : pad |
| + | * --cskip : skip |
| + | * --chardClip : hard clip |
| + | * --csoftClip : soft clip |
| | | |
| + | Use --nonM to keep any read that has a non M/X/= Cigar operator. |
| | | |
− | = Usage = | + | == Optional General Parameters == |
− | ./bam findCigars --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [--cinsert] [--cdel] [--cpad] [--cskip] [--chardClip] [--csoftClip] [--nonM] [--noeof] [--params]
| |
| | | |
| + | {{paramsParameter}} |
| + | {{noeofBGZFParameter}} |
| + | {{PhoneHomeParameters}} |
| | | |
| = Return Value = | | = Return Value = |