Currently the "Log in with Google" button redirects you to a "Page not found." This is an issue that our forum vendors are working on fixing. In the meantime, while on the "Page not found" you can edit the URL to delete the second gatk, firecloud, or wdl (depending on what subforum you are acessing).
If I align my bams using bwa-mem, do I still need to do local indel realignment?
I have ~2,000 whole-genome-sequencing bams that I need to move through an alignment/deduping/recalibration pipeline. I'll be using bwa-mem for the initial alignment, and I'm wondering if you would still recommend carrying out the local realignment step (downstream) for these bams, given bwa-mem does some local/gapped alignment on its own. This is an important question for our group because the local realignment (using RealignerTargetCreator & IndelRealigner) for these bams will take a significant amount of time / computational resources. If I want to call short indels using UnifiedGenotyper (rather than HC, due to number of samples), does bwa-mem for primary alignment reduce the need for local realignment downstream? Any feedback/thoughts would be much appreciated - thanks!