To build BWA-SW index select the Tools ‣ Align to reference ‣ Build Index item in the main menu. The Build Index dialog will appears. Set the Align short reads method parameter to BWA-SW.
The dialog looks as follows:
<center> <br> <img src="/wiki/download/attachments/6062169/Building Index for BWA-SW.png"/> <br> </center>
There are the following parameters:
Reference sequence — DNA sequence to which short reads would be aligned to. This parameter is required.
Index file name — file to save index to. This parameter is required.
Index algorithm (-a) — Algorithm for constructing BWT index. Available options are:
It implements three different algorithms
Colorspace (–color) — the input is read in colorspace, colors are encoded as characters A/C/G/T (A=blue, C=green, G=orange, T=red).