22 months ago by
You didn't actually ask about GATK or variant calling, but I see that in a lot of answers (and that is part of what you would probably want to do on the cloud).
I didn't run BWA-MEM on the cloud, but here are some thoughts:
1) I think the best solution depends upon the total number of samples. Right now, I believe you can get a $300 credit to test Google Cloud. So, if you only plan to process a limited number of samples that can essentially be free.
2) For some people, I think precisionFDA may be an acceptable solution (I believe they already have apps for BWA-MEM alignnment and GATK variant calling). If you are willing to contribute data (I created an account with a G-mail address), analysis through DNAnexus will be free.
I have some notes about my experience with precisionFDA in this blog post.
3) If you don't use precisionFDA (and instead use AWS or Google Cloud, post-credit), my limited testing gives me the impression that the costs may be a little higher than you may expect. For example, I spent a few hundred dollars getting used to AWS (although that may still have been less than a formal class), and I have some notes about running DeepVariant on Google Cloud (and AWS) here.
However, the long-term costs are something other users may admittedly be able to better to answer than myself.
I hope this helps!