They key is 23andMe was not using bleeding-edge nightly builds but official "upgrade-recommended" releases. GATK currently has no concept of a "stable" branch

They key is 23andMe was not using bleeding-edge nightly builds but official "upgrade-recommended" releases. GATK currently has no concept of a "stable" branch of their repo (Appistry is going to provide quarterly releases in the future, which is great). The flag I am raising is that a "stable" release is needed before it get's integrated into a clinical pipeline. Because the Broad's reputation is so high, it is important to raise this flag as otherwise researchers and even clinical bioinformaticians assume choosing the latest release of GATK for their black-box variant caller is as safe as an IT manager choosing IBM.