This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
FYI, in the following page: http://gatkforums.broadinstitute.org/gatk/discussion/1268/what-is-a-vcf-and-how-should-i-interpret-it
Line: "See the Tool Documentation for more details on AD (DepthPerAlleleBySample) and DP (Coverage)for more details."
The links are broken.