Question: DNA-seq PE150 BWA alignment
gravatar for zhuozhu132
3.2 years ago by
United States
zhuozhu13230 wrote:

Hi there! We sequenced some chicken genomic DNA (Illumina TruSeq, PE150), and I am trying to map the reads to reference genome with BWA mem and then call SNPs with GATK. I used the default settings of BWA, and checked the alignment statistics by using samtools flagstat. I got a 99% mapping rate. Does this mapping rate seem to be in normal range? I'm very new to DNA-seq alignment. It would be great if you guys could give me some suggestions about adjusting BWA parameters for PE150. Any input will be appreciated!

sequencing alignment • 1.2k views
ADD COMMENTlink modified 3.1 years ago • written 3.2 years ago by zhuozhu13230
gravatar for Daniel Swan
3.2 years ago by
Daniel Swan13k
Aberdeen, UK
Daniel Swan13k wrote:

I don't see any reason why you shouldn't see this kind of alignment rate at all.  We would expect to achieve this with our mammalian sequencing projects.

I'm sure the default settings for bwa mem are fine for your application.  

I'd suggest FreeBayes for your genotyping - it will probably save you some time and effort over GATK.

ADD COMMENTlink modified 3.2 years ago • written 3.2 years ago by Daniel Swan13k
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