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Revision as of 16:46, 10 February 2015
, 16:46, 10 February 2015→BAM List File
*** 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.
=== Reference Files ===
=== Reference Files ===
