preGS.jl is a pre-genomic processor for analysis in animal breeding.

preGS.jl was based on preGSf90 by Ignacio Aguilar in the BLUPF90 family of programs. You can find the documentation for preGSf90 here.

Ignacio is a very talented programmer and scientist and this is my poor starting attempt at copying his program in Julia from scratch. I'd like to write it in a way that is more flexible from the beginning, such as input formats and output formats. Ignacio has incorporated some of this into his package.

I'm not making this a package through the package manager quite yet, but in time I hope I can make it available through the package manager. To make it easier. For now, you can simply copy the function to your own computer.

Currently I use this format

julia preGS.jl input.jl

Where the input.jl file will read in all of the inputs you need like a parameter file. I don't know how to write a simpler one at this time.

Currently accepts only a simple format like preGSf90. Only the animal ID in column 1 and the string of genotypes in

SIRE_100     201200201020100202
SIRE_200     201200201010221222
...
DAM_001      101200021002020102

Simply the SNP name, the chromosome (1,2,...,n) in integer form, and position on chromosome (integer form).

SNP-5051042 1 10232
SNP-0510203 1 10400
...
SNP-2004134 18 1401020

I'm trying to allow for many options to be fairly diverse in it's ability to do things. Right now I have you read in a 'parameter file' of sorts to set the options. Hopefully it's easier than setting 100 options through the function.

I have only tested this on Ubuntu 16.04 (Linux). I will continue to test on other computers as I have time.

Always welcome. Please drop me an email at [email protected]

Thanks for visiting my page. Please see others.