Question: Which simulation software do you recommend to generate SNP if I want to study GWAS, with population structure?
gravatar for haohanw
2.9 years ago by
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 • 1.5k views
ADD COMMENTlink modified 7 months ago by azzaea0 • written 2.9 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 7 months ago by azzaea0

Yes, I used SimuPop ( 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 7 months 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 7 months ago by azzaea0

Hi, Thank you for your interest in our work. This is my recent work ( 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 7 months 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 7 months 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 7 months ago by haohanw90
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1152 users visited in the last hour