BWA aln _ option for number of mismatch ???

[Sam64]

Hi,
What is the option which allows to select the number of mismatch accepted in a read? Please, anybody could help me by giving an example ?
Regards,
Sam64

[cjp]

Maybe you can only do it in the seeded alignment.


% bwa aln

Usage: bwa aln [options] <prefix> <in.fq>

Options: -n NUM max #diff (int) or missing prob under 0.02 err rate (float) [0.04]
-o INT maximum number or fraction of gap opens [1]
-e INT maximum number of gap extensions, -1 for disabling long gaps [-1]
-i INT do not put an indel within INT bp towards the ends [5]
-d INT maximum occurrences for extending a long deletion [10]
-l INT seed length [32]
-k INT maximum differences in the seed [2]
-m INT maximum entries in the queue [2000000]
-t INT number of threads [1]
-M INT mismatch penalty [3]
-O INT gap open penalty [11]
-E INT gap extension penalty [4]
-R INT stop searching when there are >INT equally best hits [30]
-q INT quality threshold for read trimming down to 35bp [0]
-c input sequences are in the color space
-L log-scaled gap penalty for long deletions
-N non-iterative mode: search for all n-difference hits (slooow)
-f FILE file to write output to instead of stdout

The -n option maybe what you want here - if you set it to an integer.

Also:

-k is for the number of mis-matches in the seed alignment and -l is for the length of the seed alignment, - so maybe you can change -l to the length of your read and -k to whatever you want. Otherwise try lowering -M to get less of a penalty for mis-matches.

Chris

[Sam64]

Thank you for your post
It helped me a lot