Which simulation software do you recommend to generate SNP if I want to study GWAS, with population structure?
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7.3 years ago
haohanw ▴ 90

I want to generate the SNP data, so that I can start to test my statistical model. The primary problem my model works on is the population stratification, so that I hope the simulation can add some population structure into it.

In addition, I hope that the underlying population structure could be known so that I can check if my method works.

I found a lot of them here: List of Genetic Simulation Resources

Which one do you recommend?

GWAS SNP software • 3.5k views
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I'm wondering if you ever settled on a simulator- or if you had publications/preprints of your work that you may share? Thanks

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Yes, I used SimuPop (http://simupop.sourceforge.net/) eventually. It's a quite powerful python software. I have publications on the method side for the population stratification and association study, not sure if you are interested.

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Hi again. Nice- thank you. Please do share. I'm VERY interested in your method. PS:- for some reason biostar didn't send a notification with your response- Looking at my user settings to avoid this in the future. Thanks again, Azza

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Hi, Thank you for your interest in our work. This is my recent work (https://www.biorxiv.org/content/10.1101/336727v2) that we have put a lot of thoughts on it. I hope you will like it. (Sorry for a delayed reply, I was putting the latest version of the article onto BioXiv after I saw your message since I personally think this work is more worth sharing even than my previously accepted work :-D )

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Nice- thank you! And Congratulations actually! I shared the pre-print on Twitter now. The problem angle and approach is quite innovative honestly, so I have my hard copy in hand now :)

The simulation scenario (for X1, just a single dataset) is pretty much what I like to have. Do you have its code roughly available for sharing too? Doesn't need to be well polished.

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Thank you for your nice words. Sure, I'm happy to share the codes if you shoot me an email about this. I would always love to help and discuss other related research projects.

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