how to specify path to precalculated bwa index files?

[mcnach]

Hi everyone, this is my first post (fanfare sounds )

I want to align a series of pair end reads, which I was shown I could do like this:

bwa mem -M -t 30 /...path omitted.../ucsc.hg19.fasta \
file1.fq.gz \
file2.fq.gz \
> aligned_sample1.sam

and that works fine, as the bwa index files are in the same folder as the reference ucsc.hg19.fasta file.

HOWEVER, I now have a series of mouse files, and the reference fasta file and the bwa index files are not in the same folder. I'm logged into a central server to do this work, and the admin has stored the mm10.fa file say in "/...path1.../mouse/mm10/" and has calculated the index files and stored them under "/...path1.../mouse/bwa_indices/"...

so that when I try to run

bwa mem -M -t 30 /...path 1.../mouse/mm10/mm10.fa \
file1.fq.gz \
file2.fq.gz \
> aligned_sample1.sam

it fails because the index files have not been found.

I cannot write to these directories because they're protected, so I can't just move the index files to the same place as the fasta file.

As a workaround, I copied the fasta file and the bwa index files to a new directory, and worked from there. This works, but I'm duplicating data unnecessarily.

I'd like to know how I can specify different paths for the reference fasta file and the bwa index files when using bwa mem as above.
I cannot find that in the documentation, so I suspect it's a very basic question... but then I'm a total beginner on this so please be gentle

[dpryan]

Then just:

bwa mem -M -t 30 /...path1.../mouse/bwa_indices/mm10.fa file1.fq.gz file2.fq.gz > aligned_sample1.sam

Or something like that. The "mm10.fa" part is just the prefix that the files use, you don't actually need the fasta file.

[mcnach]

Then just:

bwa mem -M -t 30 /...path1.../mouse/bwa_indices/mm10.fa file1.fq.gz file2.fq.gz > aligned_sample1.sam

Or something like that. The "mm10.fa" part is just the prefix that the files use, you don't actually need the fasta file.

seriously?

it makes sense... the index files already contain the sequence information!

I told you it would be basic Thanks!