It looks like you're new here. If you want to get involved, click one of these buttons!
I have exome data run on two lanes per library is it better to combine the lanes into one or to run each lane independently through GATK? What are the pros and cons?
This is discussed in our Best Practices document.
Geraldine Van der Auwera, PhD
Thanks. I'd read that page previously, but had forgotten about it over the hols. d'oh!