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GotCloud: Alignment Pipeline

257 bytes added, 18:39, 28 January 2016
Optional Configurable Settings
* BWA_THREADS = -t N
** 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
** Maximum amount of memory used by samtools sort after running bwa

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