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, 16:46, 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 outputDirectory/bam.list. It can be overridden by setting --bamlist, --bam_list, or --list on the command-line or by setting BAM_LIST in your configuration file to the path to the BAM List File. See [[#Required Options|Required Options]] for more information. |
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| === Reference Files === | | === Reference Files === |