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adimitromanolakis / sim1000G

Simulation of rare and common variants based on 1000 genomes data
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Simulate whole samples #1

Closed jcgrenier closed 4 years ago

jcgrenier commented 5 years ago

Hello! Thanks for that tool! Is there a way to directly simulate a whole sample that will have a genetic background that will look normal? The only thing I was able to do for the moment is to simulate chromosome per chromosome, so I suppose that I won't be able to concatenate all the chromosomes together in the end without looking at weird samples.

Thanks for the help. Best,

adimitromanolakis commented 5 years ago

Hi, you can concatenate all the chromosomes, it is not a problem and will result in a normal looking sample.

Best, Apostolos

jcgrenier commented 5 years ago

Hello @adimitromanolakis , thanks for the quick answer! I'll give it a try and will come back to you if we are encountering any issues with that! Thanks!

jcgrenier commented 5 years ago

Hum, while thinking about it, how does it work exactly. How is one samples simulated? Does it take 2 different samples as parents of the samples and create a new one, or it's more random than this?

Thanks for your help!

adimitromanolakis commented 5 years ago

Depends, if you simulate independant samples then there are no parents but generated randomly based on a model of the LD and allele frequencies of the markers. If you generate family data, then 2 individuals have to be the parents.

jcgrenier commented 5 years ago

Alright, that's basically what I wanted to do. Thanks a lot for your help!