produce an alignment file to supplement the VCF output
It would be nice to have a file in a standard alignment format to represent the information in the VCF file. I've taken this idea from C-Sibelia. Code from there might be directly adaptable if it can simply use the VCF file as input.
This doesn't need to be part of this project if it ends up being a code to convert VCF to XMFA, for example.