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| but uses a lot of memory since it stores all the read names. | | but uses a lot of memory since it stores all the read names. |
| --rmTags : Remove the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type... | | --rmTags : Remove the specified Tags formatted as Tag:Type;Tag:Type;Tag:Type... |
| + | --noeof : do not expect an EOF block on a bam file. |
| + | --params : print the parameter settings |
| Quality Binning Parameters (optional): | | Quality Binning Parameters (optional): |
| Bin qualities by phred score, into the ranges specified by binQualS or binQualF (both cannot be used) | | Bin qualities by phred score, into the ranges specified by binQualS or binQualF (both cannot be used) |
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| --binMid : Use the mid point of the quality bin range for the quality value of the bin. | | --binMid : Use the mid point of the quality bin range for the quality value of the bin. |
| --binHigh : Use the high end of the quality bin range for the quality value of the bin. | | --binHigh : Use the high end of the quality bin range for the quality value of the bin. |
− | --noeof : do not expect an EOF block on a bam file.
| |
− | --params : print the parameter settings
| |
| </pre> | | </pre> |
| | | |
− | | + | == Required Parameters == |
| {{inBAMInputFile}} | | {{inBAMInputFile}} |
| {{outBAMOutputFile}} | | {{outBAMOutputFile}} |
| | | |
| + | ==Optional Parameters== |
| + | {{refFile}} |
| + | |
| + | === Keep OQ Tag (<code>--keepOQ</code>) === |
| + | Use <code>--keepOQ</code> to keep the OQ tag rather than removing it. By default, the OQ tag is removed. |
| + | |
| + | === Keep Duplicates (<code>--keepDups</code>) === |
| + | Use <code>--keepDups</code> to keep records that are marked as duplicate (in the flag). By default, records marked as duplicate are removed. |
| + | |
| + | === Replace Read Names with Unique Integers (<code>--sReadName</code>, <code>--readName</code>) === |
| + | Use <code>--sReadName</code> or <code>--readName</code> to replace read names with unique integers and write the mapping to the specified file. |
| + | |
| + | <code>--sReadName</code> requires the input file to have been presorted by readname, but no validation is done to ensure proper sorting. If it is not sorted, a readname will get mapped to multiple new values. |
| + | |
| + | <code>--readName</code> does not require the input file to have been presorted by readname, but uses a lot of memory since it stores all the read names in memory. |
| + | |
| + | === Remove Tags (<code>--rmTags</code>) === |
| + | Use <code>--rmTags</code> followed by a list of tags separated by ';' to remove the specified tags. The tags should be formatted as: <code>Tag:Type"</code> |
| + | |
| + | {{noeofBGZFParameter}} |
| + | {{paramsParameter}} |
| + | |
| + | ==Optional Quality Binning Parameters== |
| + | Optionally, Quality scores can be binned to reduce the number of possible quality scores. |
| + | |
| + | === Quality Score Bins (<code>--binQualS</code>, <code>--binQualF</code>)=== |
| + | Use <code>--binQualS</code> or <code>--binQualF</code> to bin qualities by phred score, into the specified ranges (only one of the two options can be specified). |
| + | |
| + | The ranges are specified by comma separated minimum phred score for the bin, example: 1,17,20,30,40,50,70 |
| + | |
| + | The first bin always starts at 0, so does not need to be specified. |
| + | |
| + | By default, the bin value is the low end of the range. Use [[#Quality Score Bin Value (--binMid, --binHigh)|<code>--binMid</code> or <code>--binHigh</code>]] to change the value for the bin. |
| + | |
| + | Use <code>--binQualS</code> followed by the comma-separated bin minimum phred scores to specify the ranges on the command line. |
| + | |
| + | Use <code>--binQualF</code> followed by the filename to specify the ranges in a file. |
| + | |
| + | === Quality Score Bin Value (<code>--binMid</code>, <code>--binHigh</code>)=== |
| + | By default the lowest number in a bin is used as the bin's value. |
| + | |
| + | Use <code>--binMid</code> to use the mid point of the quality bin range for the quality value of the bin. |
| + | |
| + | Use <code>--binHigh</code> to use the highest number in the quality bin for the quality value of the bin. |
| | | |
| | | |
| + | {{PhoneHomeParameters}} |
| | | |
| = Return Value = | | = Return Value = |
− | Returns the SamStatus for the reads/writes. | + | Returns the SamStatus for the reads/writes (0 for success, non-0 for failure). |
| | | |
| | | |