Can You Use Flapjack To Group Individuals Into Cultivars?

Question

[Philipp Bayer]

Hi everyone,

I'm currently trying to "learn" Flapjack (http://bioinformatics.oxfordjournals.org/content/26/24/3133.full) and something got me stumped:

I've got roughly 40 genotypings from plants belonging to either of 2 cultivars, is there any way to use Flapjack to visualise to which cultivar which individual belongs, based on SNPs?

Answer 1

[Fabio Marroni]

I would suggest that you assign yourself individuals to a population (based on the SNPs) and then code the population as a binary phenotype. You can then choose to change color based on phenotype. You can also sort individuals by genetic distance, but I don't know how flapjack calculates it.