Hi guys,
I am going to use BWA and GATK to detect SNPs and small indels in one of my projects. This is my first time to use BWA. I would like to know what are the parameters you guys use for BWA? Which parameter is associated with uniquely mapped/best quality reads?
Thank you very much.
I am going to use BWA and GATK to detect SNPs and small indels in one of my projects. This is my first time to use BWA. I would like to know what are the parameters you guys use for BWA? Which parameter is associated with uniquely mapped/best quality reads?
Thank you very much.