Question: convert MACH .mlprob to Oxford .gen format
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gravatar for Ahill
3.5 years ago by
Ahill1.5k
United States
Ahill1.5k wrote:

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.

plink mach • 1.1k views
ADD COMMENTlink modified 3.3 years ago by Biostar ♦♦ 20 • written 3.5 years ago by Ahill1.5k
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