bwa index output files
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3.2 years ago

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

Assembly bwa indexing • 3.6k views
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What is the exact command you used?

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bwa index file.fa
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3.2 years ago
ATpoint 55k

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.

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3.2 years ago

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

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