Bwa Specify Number Of Maximum Mismatches And Gaps

Question

[Nicolas Rosewick]

Hi,

With bwa, how can I specify the number of maximum mismatches and gaps in bwa ? I try to play with the -o and -e parameters but it didn't change anything. For info, I'm working on short read ~ 25 bp (single-end)

More general question : Which aligner for short read with gap and mismatch allowed

Thanks,

N.

[Michael]

there was a similar question here where I explained the -n parameter: http://biostar.stackexchange.com/questions/16267/what-does-bwas-n-parameter-mean

Answer 1

[Michael]

http://bio-bwa.sourceforge.net/bwa.shtml

The -n parameter controls edit distance in particular.

[Nicolas Rosewick]

I don't understand this -n parameter

what is the result of doing -n 1 or -n 0.05 or -n 4

Thanks

[Michael]

Do you mean this:

-n NUM Maximum edit distance if the value is INT, or the fraction of missing alignments given 2% uniform base error rate if FLOAT. In the latter case, the maximum edit distance is automatically chosen for different read lengths. [0.04]

[Nicolas Rosewick]

yes I it's a little bit confused for me