Run Monopogen on other species

[qiqi277]

Dear Monopogen developers ,
I only intended to do Germline SNV calling. I had some population genetic data for my species (over 2000 individuals) and constructed the reference panel accordingly, but the precision of my germline variation testing results was not ideal. So I wanted to ask, if I want to run Monopogen on other species, what other information do I need to consider besides changing the reference panel? Here is my run command.
python ${Monopogen_path}/src/Monopogen.py preProcess -b $output/bam.lst -o $output -a ${Monopogen_path}/apps -t 18 && echo " m1 completed." || echo "m1 failed."
python ${Monopogen_path}/src/Monopogen.py germline -r $dir/region.lst -s all -o $output -g $ref -p $REGION_VCF -t 18 \ -a ${Monopogen_path}/apps && echo " m2 completed." || echo "m2 failed."