Advice re multi-lane samples

drchriscole

Hi,

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? Many thanks

Geraldine_VdAuwera

This is discussed in our Best Practices document.

http://www.broadinstitute.org/gatk/guide/article?id=1186

drchriscole

Thanks. I'd read that page previously, but had forgotten about it over the hols. d'oh!