Question

State of the art GWAS tools

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9.9 years ago

jth ▴ 190

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 • 3.9k views

ADD COMMENT • link updated 10 months ago by Ram 43k • written 9.9 years ago by jth ▴ 190

Ram · Answer 1 · 2014-06-05

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9.9 years ago

Maxime Lamontagne ★ 2.3k

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

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

ADD COMMENT • link updated 3.1 years ago by Ram 43k • written 9.9 years ago by Maxime Lamontagne ★ 2.3k

Ram · Answer 2 · 2014-06-05

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9.9 years ago

johnstantongeddes ▴ 410

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

ADD COMMENT • link updated 3.1 years ago by Ram 43k • written 9.9 years ago by johnstantongeddes ▴ 410

score 2 · Answer 3 · 2016-03-11

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8.1 years ago

Hongxu Dong ▴ 40

rrBLUP package is a good one.

ADD COMMENT • link 8.1 years ago by Hongxu Dong ▴ 40

score 2 · Answer 4 · 2016-03-13

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8.1 years ago

Hongxu Dong ▴ 40

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

ADD COMMENT • link 8.1 years ago by Hongxu Dong ▴ 40

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

ADD REPLY • link 7.3 years ago by Ram S ▴ 60