Question: Create An Index With Samtools Within A Pipeline?
1
Joshua Orvis • 100 wrote:
I want to make a pipeline that grabs a reference genome, indexes it,
then
aligns reads to it via bwa. The bwa tool has a menu option for using
an
index "from the history" (see attached image) but I don't see any
option
within the bwa wrappers to actually create an index on the fly. This
is
also true for samtools and other aligners. The following link
describes
the conf/loc files required to add indexes to the system:
http://wiki.galaxyproject.org/Admin/NGS%20Local%20Setup
But how can they be created dynamically in the course of a pipeline
run
instead of preconfigured in this way?
Regards -
Joshua