the title says it all: I have plink compatible ped/map (bim/bam/fam) data and want to compare this genotype data with imputed data and I also want to do linear and logistic regression analysis with ProABEL (for beeing compatible with former analysis it must unfortunatly be ProbABEL). For doing this I want to convert my ped/map files to dosage (.dose) format, but havent found a tool, that can do this automatically. Scripting it by hand will cost me days. Do you know of any tool, that can convert from ped to dose?
btw, I know, that the dosages, that will be outputted can only be concrete numbers 0,1,2, thats ok. Furthermore I know f. e. gtool (http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html), but it converts to file format compatible with Impute and SNPtest only.
Thank you all in advance, any hint is helpful :) Best, Matthew