Hi Olga and Neva,
sorry if I've missed a thread on this, but Is there a classic correct way to deal with defining boundaries of sex chromosomes which show partially duplicated sequences in JBAT? It seems that overlapping chromosome boundaries and copy/pasting to duplicate are not possible and would probably be harmful options for most uses.
I guess removing and adding chromosome boundaries and patching them together from two assembly definitions could work. Or go through the diploid.sh after the rather tedious production of vcf-files with gatk etc.
What would you recommend?
Nayden