Question: bwa index output files
0
gravatar for Inquisitive8995
18 months ago by
Inquisitive8995140 wrote:

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

indexing bwa assembly • 1.7k views
ADD COMMENTlink modified 18 months ago by ATpoint28k • written 18 months ago by Inquisitive8995140

What is the exact command you used?

ADD REPLYlink written 18 months ago by RamRS25k
bwa index file.fa
ADD REPLYlink modified 18 months ago by RamRS25k • written 18 months ago by Inquisitive8995140
2
gravatar for ATpoint
18 months ago by
ATpoint28k
Germany
ATpoint28k wrote:

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.

ADD COMMENTlink written 18 months ago by ATpoint28k
2
gravatar for Devon Ryan
18 months ago by
Devon Ryan93k
Freiburg, Germany
Devon Ryan93k wrote:

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

ADD COMMENTlink written 18 months ago by Devon Ryan93k
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