HPV virus in human genome

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

hpv gatk pathseq cancer

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written 2.0 years ago by chictu •

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