Convert MACH (imputation) file formats to .gen file format

Question

[anamaria]

Hello,

How I would convert output files from MACH (.mldose, .mlinfo...) to .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

Thanks
Ana

[Ram]

Please use the formatting bar (especially the code option) to present your post better. You can use backticks for inline code (`text` becomes text), or select a chunk of text and use the highlighted button to format it as a code block. I've done it for you this time.

[anamaria]

Thanks for pointing that out, yes I will!