Should I use the same reference indexing command of bwa for WGS and WES analysis?

Question

[maria2019]

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.

Answer 1

[finswimmer]

Hello,

-a bwtsw describes the algorithm used for constructing the Burrow-Wheeler-Tree of the reference genome. bwa uses different ones for "short" and "long" genomes (Where ever the border is ...). So this is independent of the analysis you are planning.

If you just omit the -a parameter bwa will should the best algorithm automatically.

fin swimmer