Reference mapped bestRAD loci and merging paired loci

[Mason Linscott]

Hi all,

Sorry if this is posted twice or if this feature has already been implemented. I sent this out last week but it may have been filtered.

To be brief - I am trying to generate gene trees for my RAD loci using the fasta-sample output from populations. After running through the ref_map.pl pipeline for a bestRAD dataset using sbfI as the restriction enzyme, I noticed in the catalog output that many loci are just 3bp apart on the scaffold/chromosome on opposite strands. This is expected for my dataset as a single sbfI cut site can produce two fragments for sequencing and 3bp is the expected distance between fragments on opposite ends of the sbfI site. 

As larger loci are better for gene tree construction, I was looking for a flag that would enable for these 'separate' loci to be output together as a single locus. While it appears not all samples share the same locus pair but there is a fair degree of concordance across loci pairs.

Is there a flag to merge these loci together? I am planning on creating my own script for doing so but thought I would ask/request it as a feature going forward.

All the best,

Mason