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  • Aligning Short Reads with BWA-MEM

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Mismatch penalty (-B) - mismatch penalty. The sequence error rate is approximately: {.75 * exp[-log(4) * B/A]}. 

Gap open penalty (-O) - gap open penalty. 

Gap extention penalty (-E) - gap extension penalty. A gap of length k costs O + k*E (i.e. Gap open penalty is for opening a zero-length gap). 

Penalty for clipping (-L) - clipping penalty. When performing SW extension, BWA-MEM keeps track of the best score reaching the end of query. If this score is larger than the best SW score minus the clipping penalty, clipping will not be applied. Note that in this case, the SAM AS tag reports the best SW score; clipping penalty is not deducted. 

Penalty unpaired (-U) - penalty for an unpaired read pair. BWA-MEM scores an unpaired read pair as scoreRead1+scoreRead2-INT and scores a paired as scoreRead1+scoreRead2-insertPenalty. It compares these two scores to determine whether we should force pairing. 

Score threshold (-T) - don’t output alignment with score lower than score threshold. This option only affects output.

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