Question: bwa mem mismatch option
1
gravatar for Varun Gupta
3.1 years ago by
Varun Gupta900
United States
Varun Gupta900 wrote:

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

bwa mem • 2.3k views
ADD COMMENTlink modified 3.1 years ago • written 3.1 years ago by Varun Gupta900
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 758 users visited in the last hour