I've seen earlier threads on numerous permutations of MACH/PLINK/Oxford data conversions. I'd like to convert a set of several thousand MACH .mlprob/.mlinfo files to an Oxford format fileset (.gen, .sample files) while retaining the fractional genotype probabilities. Oxford format would be a better fit with another pipeline we are using. I have several thousand one-line .mlprob files, each representing all markers on one chromosome from one individual. All solutions I've seen so far seem to involve converting via a PLINK .bed/.ped intermediary, which I assume would make hard genotype calls along the way and thus lose the probability information? I'm not clear that GenAbel could readily do this? Seeking to avoid re-inventing this wheel before writing new scripts. Thanks for any suggestions.
