State of the art GWAS tools

Question

[jth]

I am curious on which tools the Biostars community uses for their GWAS analyses. They can be both commercial, or free software. My old lab used to use Golden Helix SNP & Variation Suite, but we want to cut off the costs here, even though we have a reasonable budget for software.

Thank you very much for help!

Answer 1

[Maxime Lamontagne]

PLINK (version 1.07 or the new version under development 1.90).

You can always use R and Bioconductor (http://www.bioconductor.org/).

Answer 2

[johnstantongeddes]

Though more targeted towards quantitative traits and genomic prediction, TASSEL and GAPIT (R based) are both reasonable open-source options.

Answer 3

[Hongxu Dong]

rrBLUP package is a good one.

Answer 4

[Hongxu Dong]

If you're working on polyploid, you can also try R package GWASpoly.

[Ram S]

GWASpoly can handle any ploidy not only polyploid (2x to any) ! also supports different genetic models (dominant, recessive, general etc)