question about regionStart - regionEnd

[aheritas]

Hi Robbie, This is my first time using QUILT, so I apologise if these are naive questions. I am in the first step, preparing and reformatting the reference panel. I would like to do that for each chromosome. I have downloaded the reference haplotype, legend and genetic maps from: https://mathgen.stats.ox.ac.uk/impute/1000GP_Phase3.html (I would also appreciate your views if you think these are ok for an initial genome-wide test)

However I am unsure about what I should be inputing in these parameters: --regionStart= --regionEnd= . I would think that that would correspond to the start (1) to end (length) of each chromosome, but I am not sure. I am also not sure if leaving the default behaviour of leaving these parameters blank would allow QUILT to recognize that the entire chromosome should be read.

Thank you in advance for your time and for developing this tool.