HPV virus in human genome

Question

[chictu]

Hi, I am wanting to detect if a specific patient was infected by HPV. I have both DNA and RNA sequencing for these patients. If I want to use Pathseq from GATK,

• should I use RNA or DNA as the input for host genome? I know they used RNA in this study, but why not DNA when it might be integrated into the genome?
• is there a way to distinguish the patients with virus integrated in the genome and those that's exogenous