I am wondering the best way to convert a Multiple Alignment Format file (MAF) generated with Mugsy (http://mugsy.sourceforge.net/) into a VCF format for downstream analysis?
I have looked through past posts and haven't found an answer. It seems that there was an earlier branch of Biopython which could do this but I don't think it is being updated.
If anyone has suggestions, that would be incredible! Thank you!