This is illegal in France but let's assume I did it and have a file with the sequencing - what build I do with it?
Are there public web sites which you can use to get an analysis?
Assume a PhD in physics level, with courses on microbiology (cytology mostly) and ecology and a will to learn. I think I am asking about how to "bootstrap" the process having the data in hand.
What is illegal in France?
>Are there public web sites which you can use to get an analysis?
For example, Promethease. Takes you from a SNP array to results in a few minutes.
> How to "bootstrap" the process
The easiest thing you can do is to calculate your HLA/MHC haplotypes and then infer the risk of many common infectious and autoimmune disorders. This region has most of the common associations with biggest effect sizes.
Also easy, filter high quality rare variants and go to something like gnomAD. Then try to find rare ones with a big impact, i.e. those generally linked to Mendelian diseases. It'd be weird to find anything interesting here, as you would already know.
Easy, doable with a SNP array only, no full genome needed. Take some marker SNPs, and calculate your admixture using some topic model, usually LDA. This gives you your ancestry.