I am trying to use --cojo-slct to 'Perform a stepwise model selection procedure to select independently associated SNPs. Results will be saved in a .jma file with additional file .jma.ldr showing the LD correlations between the SNPs.'
According to the paper,
Start with a model with the most significant SNP in the single-SNP meta-analysis across the whole genome with P value below a cutoff P value, such as 5 × 10–8.
For the tth step, calculate the P values of all the remaining SNPs conditional on the SNP(s) that have already been selected in the model. To avoid problems due to colinearity, if the squared multiple correlation between a SNP to be tested and the selected SNP(s) is larger than a cutoff value, such as 0.9, the conditional P value for that SNP will be set to 1.
Select the SNP with minimum conditional P value that is lower than the cutoff P value. However, if adding the new SNP causes new colinearity problems between any of the selected SNPs and the others, we drop the new SNP and repeat this process.
Fit all the selected SNPs jointly in a model and drop the SNP with the largest P value that is greater than the cutoff P value.
Repeat processes (2), (3) and (4) until no SNPs can be added or removed from the model.
To know the order of SNPs selected by --cojo-slct, can I rank them according to the *.jma file after selecting out the most significant SNP.
I am trying to use --cojo-slct to 'Perform a stepwise model selection procedure to select independently associated SNPs. Results will be saved in a .jma file with additional file .jma.ldr showing the LD correlations between the SNPs.'
According to the paper,
To know the order of SNPs selected by --cojo-slct, can I rank them according to the *.jma file after selecting out the most significant SNP.
Thank you