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Bwa Specify Number Of Maximum Mismatches And Gaps

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.

bwa
• 9,656 views • link
updated by Michael Dondrup Michael Dondrup • written by Nicolas Rosewick Nicolas Rosewick

1 answer

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

The -n parameter controls edit distance in particular.

• 1 views • link
updated by Ram Ram • written by Michael Dondrup Michael Dondrup

I don't understand this -n parameter

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

Thanks

• 0 views • link
updated by Ram Ram • written by Nicolas Rosewick Nicolas Rosewick

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]

• 0 views • link
updated by Ram Ram • written by Michael Dondrup Michael Dondrup

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