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, 14:06, 6 January 2014
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| --checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option | | --checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option |
| </pre> | | </pre> |
| + | {{PhoneHomeParamDesc}} |
| | | |
| + | == Required Parameters == |
| + | {{InBAMInputFile}} |
| + | {{OutBAMOutputFile}} |
| + | |
| + | == Optional Parameters == |
| + | === Verbose (<code>--verbose</code>) === |
| + | Use <code>--verbose</code> to turn on verbose mode. |
| + | |
| + | === Specify Log Filename (<code>--log</code>) === |
| + | Use <code>--log</code> followed by the log filename to specify the log filename. Default is the output file basename with a <code>.log</code> extension |
| + | |
| + | === Add the HD Header (<code>--HD</code>) === |
| + | Use <code>--HD</code> followed by the HD header line to add a HD header. Be sure to include "@HD" in the line you specify. |
| + | |
| + | === Add the RG Header (<code>--RG</code>) === |
| + | Use <code>--RG</code> followed by the RG header line to add a RG header. Be sure to include "@RG" in the line you specify. |
| + | |
| + | === Add the PG Header (<code>--PG</code>) === |
| + | Use <code>--PG</code> followed by the PG header line to add a PG header. Be sure to include "@PG" in the line you specify. |
| + | |
| + | === Add MD5 and UR tags to SQ Headers (<code>--fasta</code>) === |
| + | Use <code>--fasta</code> followed by the fasta reference file name to compute MD5sums and update SQ tags with the M5 & UR values. Use the [[#Add the UR tag to SQ Headers (--UR)|<code>--UR</code>]] option to specify a different UR value. |
| + | |
| + | === Add the AS tag to SQ Headers (<code>--AS</code>) === |
| + | Use <code>--AS</code> followed by the genome assembly identify to add the AS tag to the SQ Headers. |
| + | |
| + | === Add the UR tag to SQ Headers (<code>--UR</code>) === |
| + | Use <code>--UR</code> followed by the URI of the sequence to add the UR tag to the SQ Headers. |
| + | |
| + | The UR header will be automatically added with the [[#Add MD5 and UR tags to SQ Headers (--fasta)|<code>--fasta</code>]] option, so if [[#Add MD5 and UR tags to SQ Headers (--fasta)|<code>--fasta</code>]] is used, <code>--UR</code> only needs to be specified if it is different from [[#Add MD5 and UR tags to SQ Headers (--fasta)|<code>--fasta</code>]]. |
| + | |
| + | === Add the SP tag to SQ Headers (<code>--SP</code>) === |
| + | Use <code>--SP</code> followed by the species to add the SP tag to the SQ Headers. |
| + | |
| + | {{PhoneHomeParameters}} |
| | | |
| = Return Value = | | = Return Value = |
− | Returns 0. | + | Returns 0 on success, non-0 on failure. |
| | | |
| = Example = | | = Example = |
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| </pre> | | </pre> |
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| + | |
| + | [[Category:BamUtil|polishBam]] |
| + | [[Category:BAM Software]] |
| [[Category:Software]] | | [[Category:Software]] |
− | [[Category:StatGen Download]]
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− | [[Category:BAM Software]]
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