bwa index output files

Question

[Inquisitive8995]

Hi, I am running bwa index and it generates several output files out of which few are binary files. The other files such as ".ann and .amb" give me output which I am not able to analyse. Is there a manual which explains the output results ? I tried looking into bwa_indexing manual but I could not find it.

The .amb output looks like this:

115169878 1 6 0 19020000 N 86760324 150000 N

Thanks for your help

[Ram]

What is the exact command you used?

[Inquisitive8995]

bwa index file.fa

Answer 1

[ATpoint]

As Devon said, there is no need to spend your time on these files. They are used by BWA internally during the alignment. These files are the burrows-wheeler-transformed genome, the suffix array index, the packed sequence etc, but unless you are interested in alignment theory, ignore them and simply do your alignment.

Answer 2

[Devon Ryan]

There's no reason to look at the output from indexing, you just use it for alignment.