Meta analysis on 2 genotyping data set

Question

[mel22]

Hi Please is there any tutorial or help on.doing meta anlysis in R on genotyping data sets ( about 300 000) SNP , three case control studies all genotype with same DNA chip, my questions are : 1/which r package do you advise me ? 2/ can you help with a detailed tutorial with different steps : data preparation tests ... 3/ is it possible to do a meta analysis on gwas data with an interaction term ? If yes how ? Thank you very much, any help is welcomed :)

Answer 1

[Sam]

Not sure for R, but a lot of people use METAL to perform meta analysis. You can refer to their manual here

[mel22]

Thank you very much Sam

Answer 2

[mel22]

It seems that to use METAL i need to have separately a file for each marker : - Is there a bash code that i can use to extract a file for each marker from a big one file ? -Is there any alternative to METAL to do this with R ( I am more used to R :( ...)

THANK YOU VERY MUCH

[Sam]

Think you only need the summary statistic files. You can follow their quick start page which provide the examples and scripts