Path to pre-indexed genome ?

Question

[marc.deloger]

Hi Pierre,

is there a manner to specifiy a path to a BWA pre-indexed genome instaed of giving a pth to the FASTA file and spend time to index it ?

Thank you

[marc.deloger]

Thank you for your answer but the fact is that I have BWA indexes in the same folder of the fasta file and it still takes time to index the genome

[Devon Ryan]

Right, but you only need to do that once.

[marc.deloger]

Sure only once but an unnecessary one, because it overwrote the pre-existing bowtie BWA indexes we already did before using DiscoSNP++, that's why I do not understand why not simply verify that an index already exist in the same folder of the FASTA file.

[Devon Ryan]

BWA and bowtie don't have compatible indices.

[marc.deloger]

My mistake, I wrote bowtie instead of BWA in the previous post.

[Devon Ryan]

BWA will generally only make an index if you type bwa index...

Answer 1

[Devon Ryan]

Just create a symlink to the fasta file from the directory with the indices. That's what we do with all of our indices.