Merge overlapping regions of a single chromosome which were phased separately

Question

[Georgi]

Hi,

I would like to speed up my phasing by splitting chromosomes into a smaller regions. Each region will have, for example, 1Mb overlap with the adjacent region. I will next phase each region separately. The question is: how can I properly merge individually phased regions into a single chromosome without introducing switch errors on the edges? I have these overlapping regions, but how to properly align their phase during the merge? Is there any tool or plugin or it should be done manually? I am using Eagle for phasing.

Thank you!