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, 18:39, 28 January 2016
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| * 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 |