I want to do WGS and WES alignment with BWA mem. Should I use the same reference indexing command for both WES and WGS?
I know that reference indexing for WGS would be: "bwa index -a bwtsw ref.fa"
- Should I use the command for the WES or I should remove the - a bwtsw and go with "bwa index ref.fa"?
- Where should I use - a bwtsw option exactly? I know that it is a must for WGS.