To build BWA index select the Tools ‣ NGS data analysis ‣ Build index for reads mapping item in the main menu. The Build Index dialog appears. Set the Align short reads method parameter to BWA.

The dialog looks as follows:

     <img src="/wiki/download/attachments/4227717/Building Index for BWA.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 BWA 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).