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Revision as of 18:39, 28 January 2016
, 18:39, 28 January 2016→Optional Configurable Settings
* BWA_THREADS = -t N
* BWA_THREADS = -t N
** Fill in the N with the number of threads you want BWA to run with, default is 1
** Fill in the N with the number of threads you want BWA to run with, default is 1
* BWA_QUAL = -q N
** Fill in the N with the trim quality you want BWA aln to run with, default is 15. This parameter is only applied to bwa aln. It is not used for BWA_MEM.
* BWA_MEM_OPTS =
** Specify any additional bwa mem options using this parameter.
* SORT_MAX_MEM = 2000000000
* SORT_MAX_MEM = 2000000000
** Maximum amount of memory used by samtools sort after running bwa
** Maximum amount of memory used by samtools sort after running bwa
