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, 12:30, 6 January 2014
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| </pre> | | </pre> |
| {{PhoneHomeParamDesc}} | | {{PhoneHomeParamDesc}} |
| + | |
| + | == Required Parameters == |
| {{InBAMInputFile}} | | {{InBAMInputFile}} |
| {{OutBAMOutputFile}} | | {{OutBAMOutputFile}} |
| | | |
| == Optional Region Specifying Parameters == | | == Optional Region Specifying Parameters == |
− | {{bamIndex|hdr====}} | + | {{bamIndex}} |
| === Read only a Specific Reference/Chromosome (<code>--refName</code> or <code>--refID</code>) === | | === Read only a Specific Reference/Chromosome (<code>--refName</code> or <code>--refID</code>) === |
| If you only want to read a specific reference (chromosome), specify either <code>--refName</code> followed by the reference name or </code>--refID</code> followed by the reference id. | | If you only want to read a specific reference (chromosome), specify either <code>--refName</code> followed by the reference name or </code>--refID</code> followed by the reference id. |
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| Left shift indels as far as they can go in the read. | | Left shift indels as far as they can go in the read. |
| | | |
− | {{paramsParameter|hdr====}}
| + | === Skip Records with any of the Specified Flags (<code>--excludeFlags</code>) === |
− | {{noeofBGZFParameter|hdr====}} | + | |
| + | Use <code>--excludeFlags</code> followed by the flags (as one integer) to skip any records that has any of the specified flags set. |
| + | |
| + | This parameter was added in version 1.0.10. |
| + | |
| + | === Only Process Records with the all of the Specified Flags (<code>--requiredFlags</code>) === |
| + | |
| + | Use <code>--requiredFlags</code> followed by the flags (as one integer) to only process records with all of the specified flags set. |
| + | |
| + | This parameter was added in version 1.0.10. |
| + | |
| + | {{paramsParameter}} |
| + | {{noeofBGZFParameter}} |
| {{PhoneHomeParameters}} | | {{PhoneHomeParameters}} |
| | | |