Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
We sequenced some chicken genomic DNA (Illumina TruSeq, 150PE) for SNP calling. I did reads alignment with BWA mem, default settings, then checked the statistic by using flagstat. The mapping rate is >99%. I'm wondering is this mapping rate normal? If not, what's your suggestions to tune bwa parameters. Thank you very much!