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| Parameter | Description | Default value |
|---|---|---|
| Output directory | Directory to save BWA-MEM output files. | |
| Reference genome | Path to indexed reference genome. | |
| Output file name | Base name of the output file. 'out.sam' by default. | out.sam |
| Number of threads | Number of threads (-t). | 1 |
| Min seed length | Path to indexed reference genome (-k). | 19 |
| Band width | Band width for banded alignment (-w). | 100 |
| Dropoff | Off-diagonal X-dropoff (-d). | 100 |
| Internal seed length | Look for internal seeds inside a seed longer than {-k} (-r). | 1.50000 |
| Skip seed threshold | Skip seeds with more than INT occurrences (-c). | 10000 |
| Drop chain threshold | Drop chains shorter than FLOAT fraction of the longest overlapping chain (-D). | 0.5 |
| Rounds of made rescues | Perform at most INT rounds of mate rescues for each read (-m). | 100 |
| Skip mate rescue | Skip mate rescue (-S). | False |
| Skip pairing | Skip pairing; mate rescue performed unless -S also in use (-P). | False |
| Mismatch penalty | Score for a sequence match (-A). | 1 |
| Mismatch penalty | Penalty for a mismatch (-B). | 4 |
| Gap open penalty | Gap open penalty (-O). | 6 |
| Gap extension penalty | Gap extension penalty; a gap of size k cost {-O} (-E). | 1 |
| Penalty for clipping | Penalty for clipping (-L). | 5 |
| Penalty unpaired | Penalty for an unpaired read pair (-U). | 17 |
| Score threshold | Minimum score to output (-T). | 30 |
Parameters in Workflow File
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