Masking strategies for SARS-CoV-2 alignments

@goldman, @NicolaDeMaio thanks for sharing this! I’m interested in apply this mask in an analysis that I’m currently working on. Do you have recommendations for software that can be used to apply a VCF mask like this to an alignment? I’m imagining providing your VCF and my aligned fasta file as input, and getting a fasta file as output with the masked positions removed.