Question

STRUCTURE software for GBS SNP data

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9.7 years ago

dinesh ▴ 50

I have GBS SNP genotyped data in .hapmap format. I want to find the population structure through structure software. please tell me how to run this software. like the input format

software-error SNP • 10k views

ADD COMMENT • link updated 21 months ago by Ram 44k • written 9.7 years ago by dinesh ▴ 50

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Relevant resource: http://pbgworks.org/sites/pbgworks.org/files/Tutorial%20of%20STRUCTURE%20software.pdf

ADD REPLY • link 2.5 years ago by Ram 44k

Ram · Answer 1 · 2015-03-02

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9.7 years ago

Brice Sarver ★ 3.8k

The manual, always a good place to answer these sorts of questions.

If you can convert your data to PLINK format, you can run ADMIXTURE. It's easier and faster to run. STRUCTURE's input files' formats are a bit of a pain in the butt.

ADD COMMENT • link updated 21 months ago by Ram 44k • written 9.7 years ago by Brice Sarver ★ 3.8k

Ram · Answer 2 · 2015-05-12

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9.5 years ago

JorgeGonzalez ▴ 20

You use this program: http://www.cmpg.unibe.ch/software/PGDSpider/

ADD COMMENT • link updated 21 months ago by Ram 44k • written 9.5 years ago by JorgeGonzalez ▴ 20