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, 16:45, 10 February 2015
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| *** only used by Thunder (part of ldrefine pipeline) | | *** only used by Thunder (part of ldrefine pipeline) |
| *** if all samples are from the same population, population label can be skipped or you can just specify <code>ALL</code> for the population label for each sample. | | *** if all samples are from the same population, population label can be skipped or you can just specify <code>ALL</code> for the population label for each sample. |
| + | |
| + | The path to the BAM List file is defaulted to the <code>outputDirectory/bam.list</code>. It can be overridden by setting <code>--bamlist</code>, <code>--bam_list</code>, or <code>--list</code> on the command-line or by setting BAM_LIST in your configuration file to the path to the BAM List File. |
| | | |
| === Reference Files === | | === Reference Files === |