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-MEM.

The dialog looks as follows:

     <img src="/wiki/download/attachments/10289163/Building Index for BWA-MEM.png"/>

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 (–c) — the input is read in colorspace, colors are encoded as characters A/C/G/T (A=blue, C=green, G=orange, T=red).