I am using bwa mem to align my paired end read data. My reads are 150bp in length(paired end). I am using bwa mem as the manual says to use it for read length greater than 70 bp.
My question is I could not find an explicit option to control the sequencing errors i.e number of mismatches. I would like to have around 5 mismatches for 150 bp read I have.
I used this bwa mem command line
/apps1/bwa/bwa-0.7.5a/bwa mem -t 12 -R '@RG\tID:$ID\tPL:illumina\tPU:$PU\tLB:$LB\tSM:$SM' -v 1 -a -M /cork/S.cerevisiae/indexes/bwa/sacCer3.fa file_1.fastq file_2.fastq > aln.pe.sam
With the above command line I am getting some times more than 11 mismatches in my 150 bp read. Because of this, the read is getting mapped with mismatches at a place where deletion should be present. Any help how to tune in mismatch error.
Also Can some one explain me the parameters
-O INT gap open penalty 
-L INT penalty for clipping 
I am using bwa-0.7.5a
Hope to hear from you soon.