How To Adjust Bwa Mem To Allow For Longer Gaps In Contig Alignment

Question

[William]

My first guess would be to adjust the gap extension parameter. But that one is already set to 1, the lowest integer. I now get multiple split alignment, that are relatively very close to each other and I would rather have more of a end to end alignment.

Algorithm options:

   -t INT     number of threads [1]
   -k INT     minimum seed length [19]
   -w INT     band width for banded alignment [100]
   -d INT     off-diagonal X-dropoff [100]
   -r FLOAT   look for internal seeds inside a seed longer than {-k} * FLOAT [1.5]
   -c INT     skip seeds with more than INT occurrences [10000]
   -S         skip mate rescue
   -P         skip pairing; mate rescue performed unless -S also in use
   -A INT     score for a sequence match [1]
   -B INT     penalty for a mismatch [4]
   -O INT     gap open penalty [6]
   -E INT     gap extension penalty; a gap of size k cost {-O} + {-E}*k [1]
   -L INT     penalty for clipping [5]
   -U INT     penalty for an unpaired read pair [17]

Answer 1

[thackl]

If you want to follow through on your idea about decreasing gap costs, you can do something like -A 2 -E 1. At least in recent versions of bwa -A (which scales options -TdBOELU unless overridden) scales all costs, while -E will overwrite the scaled value, essentially decreasing extension costs.

Answer 2

[wulj2]

Try to set -O to 20 and -E to 0