How I would convert output files from MACH (
.gen file format?
I need those
.gen files to run SNPTEST:
./snptest \ -data ./example/cohort1.gen ./example/cohort1.sample ./example/cohort2.gen ./example/cohort2.sample \ -o ./example/ex.out \ -frequentist 1 \ -method score \ -pheno bin1
My goal is to create GWAS summary statistics file. Alternatively I could use .mldose files to do that using plink. Any idea on that approach would be great.
The script which solves this problem is here: http://gengen.openbioinformatics.org/en/latest/tutorial/imputation/
Basically I would need to get a file which would look something like this:
MarkerName rsID Allele1 Allele2 Freq Beta SE P N 1:749963 rs529266287 T TAA 0.134 0.0017 0.014 0.90 113309 1:751343 rs28544273 A T 0.126 -3.5e-05 0.014 1.0 118061