I need to perform a meta-analysis of 2 GWAS studies and I need assistance with the input study files (plink --assoc.logistic) as well as the output meta-analysis file (.TBL).
- Firstly, I am not sure about the METAL script because of the format of the plink assoc.logistic files. (Script is attached)
- And secondly there are missing columns/information in the meta-analysed output file, such as CHR, POS, Allele1, Allele2. Do these columns need to be manually added?
Thanks :)
Hello Patricia
It requires a driver file at first for describing the input files, determining the strategy of meta-analysis, and naming the output files ( exactly the same as you provided in "metal_scrip.txt) then you need an input file with certain columns ( allele1,allele2, OR, P-value, SD, and weight column)
For making an input file you need to extract the required information of the top or the specific subset of SNPs from the 2 GWASs results from Original long data format file which contains alleles, position, and chromosome by specifying the SNPs ID and matching them together as an input file. Finally running METAL.
All the best
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