SARS-CoV-2 problematic sites

If people use sequences from GISAID, there are some known "problematic sites" in some of their genomes. See this post on [virological](https://virological.org/t/masking-strategies-for-sars-cov-2-alignments/480/12) and the associated [Github repository](https://github.com/W-L/ProblematicSites_SARS-CoV2).