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State of the art GWAS tools

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!

snp gwas
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updated by Ram Ram • written by jth jth

4 answers

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

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

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updated by Ram Ram • written by Maxime Lamontagne Maxime Lamontagne

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

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updated by Ram Ram • written by johnstantongeddes johnstantongeddes

rrBLUP package is a good one.

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written by Hongxu Dong • Hongxu Dong

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

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written by Hongxu Dong • Hongxu Dong

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

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written by Ram S Ram S

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