bwa indexed files?

[sbsusers]

Hi,

I am new to NGS. I have question on bwa indexed files.

I installed bwa-0.6.1 onto our lab server. Then I index the PhiX genome as below,
$bwa index –a bwtsw /data/genomes/PhiX/Sequence/PhiX-bwa-build/chr.fa

I also tried
$bwa index –a is /data/genomes/PhiX/Sequence/PhiX-bwa-build/chr.fa

both ways generate five files, which are (.amb, .ann, .bwt, .pac, .sa files)

But in another server from another lab, bwa (could be different version, I don't know which one) indexed files has nine files
(.fai, .rpac, .amb, .ann, .pac, .bwt, .rbwt, .rsa, .sa nine files)

I am confused on this. Can somebody explain why it happens?

Then I run alignment using bwa on same ngs reads on both server, the .sam files generated on both servers are a little different.

What should I do to make it right? Thanks a lot.

[swbarnes2]

All the genomes I have indexed (with version 0.5.9), both human genome and small bacterial genomes, have the 8 files you list above. bwa doesn't make .fai files, samtools can.

Maybe you have an older version of bwa, and you are accidently using that instead?

[sbsusers]

Thank you for the reply, swbarnes2.