I am trying to infer the relatedness of a limited set of natural accessions from the limited set of 19 genomes from the 1001 genomes of A. thaliana. This set is at http://mus.well.ox.ac.uk/19genomes/
The sequence variants for each of the 18 genomes versus the reference Col-0 accession can be found at http://mus.well.ox.ac.uk/19genomes/variants.SDI/
I want to infer the relationships amongst these accessions to find out the closest set of 5 genomes, and the most distant set of 5 genomes. I am new to asking such questions and answering them.
How do I process this sequence variation data in *.sdi files (just SNPs or even Insertions and Deletions), in order to infer relatedness of these accessions?
A faculty member at my university suggested I should use FRAPPE or ADMIXURE to process SNPs from these genomes to help answer my question. But I am unsure how I use the *.sdi data with either of these software. Could someone help please?
