Question: Create An Index With Samtools Within A Pipeline?
gravatar for Joshua Orvis
6.1 years ago by
Joshua Orvis100
Joshua Orvis100 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: But how can they be created dynamically in the course of a pipeline run instead of preconfigured in this way? Regards - Joshua
bwa alignment samtools bam • 1.2k views
ADD COMMENTlink written 6.1 years ago by Joshua Orvis100
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 178 users visited in the last hour