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!
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.