Would you be able to point out the methods (with configs) in Firecloud that could perform these two tasks (ie, Bam to uBam, uBam to realigned Bam?). It looks like there may be several good methods, but we are having trouble building a streamlined pipeline to do this.
Thanks so much.
Hello @aravi, I've split your comment into a separate discussion to better answer it.
For the first, BAM -> uBAM, you should use this method. It doesn't yet have a published configuration as we are still writing it, but we expect it to be finished in 1-2 weeks.
For the second, uBAM -> realigned BAM, you should use this method. It has a configuration for it in the configurations tab, so you should be all set.