Option to remove split and disc alignments?

[biobenkj]

Thank you for this awesome tool! Is it possible to output a bam that does not have the split and discordant reads if specifying -d and -s with samblaster? Thanks again!

[ttriche]

Poking this.

We'd like to add read groups for clipped, split, discordant, or properly-paired unsplit not-overly-clipped mappings in order to tabulate base modifications. Excluding discordant from the "main" properly-paired not-overly-clipped mappings is easy enough. Excluding clipped reads appears to mean using a perl script but does not appear to be a showstopper. Excluding split reads is something of a showstopper unless we reach in and heavily modify Samblaster itself. I imagine this would be a more straightforward task for someone who is exceedingly familiar with Samblaster.

It looks like the commented block starting around line 350 in samblaster.cpp touches on this -- is there a timeline for read-grouping and/or UMI support? Read grouping (split/disc/clipped/otherwise-OK) appears to be on the todo list for others as well.

Thanks for a great tool.