[etdr]

It's all command line tools, one is called samtools and another is called picard, there might be another one I'm forgetting.

The interesting this with the data is that it isn't your raw genome, it's the entire data from all the sequencing runs of 30 or whatever base pairs (I got my scan done at the 30x level which is supposed to mean that on average every base pair is read 30 times). So it's not like you can just read your DNA directly in one string (not sure why I want to do that but I like the idea of a single file containing just all my nucleotides in sequence). The next step for me, when I go back to it, is to get on the forums for those above tools and ask how to do the things I want, there are a LOT of subcommands.

[Metacelsus]

BWA and plink are other tools you're forgetting.

[boldlybold]

Welcome to the wonderful and confusing world of bioinformatics!