I recently imputed genotyped dataset using SHAPEIT and IMPUTE2. The resulting files are of the gen/sample format (Oxford). Because I am using the latest 1000 genome reference dataset I end up with massive gen files : chr is ~130 Gb. I would like to reorder the ids in the produced gen/sample file. looked in software such as GTOOL or QCTOOL for such options but I cannot find any.
Is anyone aware of a software that could do such a thing or do I have to code something myself?