this might be a note if nothing else. i run this in the standard non umi workflows in accordance with the ccdg spec, but I think this was mostly to run lumpy...which I have plans to run. I don't know if any other programs specifically need this. with umi, i think mate flags are superfluos when marking duplicates as umi aware. in any case, i plan on keeping this for non-umi somatic workflows.
this might be a note if nothing else. i run this in the standard non umi workflows in accordance with the ccdg spec, but I think this was mostly to run lumpy...which I have plans to run. I don't know if any other programs specifically need this. with umi, i think mate flags are superfluos when marking duplicates as umi aware. in any case, i plan on keeping this for non-umi somatic workflows.