Question: Which simulation software do you recommend to generate SNP if I want to study GWAS, with population structure?
2
gravatar for haohanw
2.3 years ago by
haohanw90
United States
haohanw90 wrote:

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?

snp gwas software • 1.1k views
ADD COMMENTlink modified 10 days ago by azzaea0 • written 2.3 years ago by haohanw90

I'm wondering if you ever settled on a simulator- or if you had publications/preprints of your work that you may share? Thanks

ADD REPLYlink written 21 days ago by azzaea0

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.

ADD REPLYlink written 20 days ago by haohanw90

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

ADD REPLYlink written 13 days ago by azzaea0

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 )

ADD REPLYlink written 10 days ago by haohanw90

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.

ADD REPLYlink written 10 days ago by azzaea0

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.

ADD REPLYlink written 9 days ago by haohanw90
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