Priority of chunk parameters

[leedchou]

Hi, all

There are 3 window parameters, they are --window-cm、--window-mb、--window-count. I am wondering what's the priority among them.

Thank you.

[srubinacci]

Hi,

There's no ordering. It's an AND of those. If a chunk does not respect any of them, it'll be sliced (except maybe for borders or other corner cases).

Best,
Simone

[leedchou]

Thank you @srubinacci very much for your quick response. I really appreciate your time.

After further reflection on your paper and running GLIMPSE2, I have a few additional questions that I would like to ask. Firstly, regarding the 3 window parameters mentioned previously, I was wondering the role and purpose of genetic map in chunk step. Could you please elaborate on how and which information in genetic map was used when doing chunk?

Moreover, I am still slightly confused about the buffer-related parameters, e.g. --buffer-cm, what does it mean? What's the difference between buffer and window?

Lastly, the output results of chunk contain 8 columns of information in each line, however, I am not aware of what these information represent. Could you possibly provide a further explanation about the 8 columns to help me better understand it?

Thank you again for your time in addressing my queries, your insights are invaluable to me.

Best regards,
Leed