Hi Everyone,

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 [6]
-L INT     penalty for clipping [5]

I am using bwa-0.7.5a

Hope to hear from you soon.

Regards
Varun