liftOver

Miotto in his Nature Genetics paper provides SNP allele counts that define each of his subgroups. Unfortunately, the coordinates in this table are based on the v2 genome (I think; it's v5.5), while ours are based on the v3 genome (v13.0). Talked to Susanne at PlasmoDB and she said there's not a great way of converting between these coordinates within PlasmoDB, but she suggested I perform a "liftover" of coordinates from v2 to v3. Generating the "chain file" needed for this can be complicated, but I found that the group from Sanger has already done this and made it available on their website. Downloaded the chain file, grabbed the pre-compiled executable (for a Ubuntu 12.xx environment) and had to install sudo apt-get install libmysqlclient-dev on my laptop.