Skip to content

Scripts Reference implementations

Jump to bottom Edit New page
Keiran Raine edited this page Apr 2, 2014 · 1 revision

The scripts detailed here are reference implementations of various mapping and analysis algorithms.

They have been built in such a way that they can be run in two modes:

  1. Fire and forget - end to end processing using single command
  2. Farm friendly - additional command line args allow specific steps to be triggered in isolation

bwa_aln.pl

Runs BWA aln+sampe method of mapping (AKA: BWA backtrack). Processes multiple lanes, merges, marks duplicates and provides completed sample BAM file including index and md5.

The default installation of PCAP-core will not install the required version of BWA for this step (0.6.2). If you wish to use this you will need to build and make this available on you path.

bwa_mem.pl

Runs 'BWA mem' method of mapping. Processes multiple lanes, merges, marks duplicates and provides completed sample BAM file including index and md5.

Add a custom footer
Add a custom sidebar

Clone this wiki locally