personalize genome

[beaferbl]

Hi,
I wanted to know how can I change the -r and -e arguments before running qsub step 1. I see that after running run_preprocess.py several qsub files are generated for each sample. I want to change the -r genome/hg19.fa and -e genome/Human_AG_all_hg19_v2.txt in the qsub1 because I have my sequences aligned in hg38. I see there is this personalize.py script; however it is not clear for me how to use it.
Best,
Bea