Thanks @goldman, and thanks again for the code @conorwalker! I ran into one very minor issue with the code, but was able to fix it. I submitted a pull request with my modification here. Other than that, I didn’t notice any issues.
I will likely end up writing some code for using this VCF-based mask for use in QIIME 2-based workflows. I’ll follow up when I have that in case it’s useful for others here.
Thanks for sharing your alignment mask and initiating this work on defining a format for these!