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  • Align reads with BWA-MEM

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ParameterDescriptionDefault value
Output directory Directory to save BWA-MEM output files. 
Reference genomePath to indexed reference genome. 
Output file nameBase name of the output file. 'out.sam' by default.out.sam
Number of threadsNumber of threads (-t).1
Min seed length

Path to indexed reference genome (-k).

Band widthBand width for banded alignment (-w).100
DropoffOff-diagonal X-dropoff (-d).100
Internal seed lengthLook for internal seeds inside a seed longer than {-k} (-r).1.50000
Skip seed threshold

Skip seeds with more than INT occurrences (-c).

Drop chain thresholdDrop chains shorter than FLOAT fraction of the longest overlapping chain (-D).0.5
Rounds of made rescuesPerform at most INT rounds of mate rescues for each read (-m).100
Skip mate rescue

Skip mate rescue (-S).

Skip pairingSkip pairing; mate rescue performed unless -S also in use (-P).False
Mismatch penalty

Score for a sequence match (-A).

Mismatch penaltyPenalty for a mismatch (-B).4
Gap open penaltyGap open penalty (-O).6
Gap extension penaltyGap extension penalty; a gap of size k cost {-O} (-E).1
Penalty for clippingPenalty for clipping (-L).5
Penalty unpairedPenalty for an unpaired read pair (-U).17
Score thresholdMinimum score to output (-T).30

Parameters in Workflow File