2.1. Detection of HBV Integrations Using VIcaller

A total of 88 HCC samples with both tumor and paired normal tissues were previously analyzed using the VIcaller platform [13]. In brief, we first submitted the paired-end reads in FASTQ format to VIcaller’s “detect” function to screen for integrations of the candidate virus, i.e., HBV ({"type":"entrez-nucleotide","attrs":{"text":"NC_003977.2","term_id":"941241313","term_text":"NC_003977.2"}}NC_003977.2), with the parameters: “-d WGS -m standard -r -a -q 20”. We then validated all identified candidate HBV integrations using the VIcaller “validate” function with the default parameters. Only the successfully validated HBV integration candidates were included for further analyses. Lastly, we calculated the integration allele fraction of each detected HBV integration event using the VIcaller “calculate” function with default parameters. To identify novel HBV integration events in the 88 HCC samples, we subsequently compared our detected HBV integrations with those presented by Sung et al. [9]. The resulting HBV integrations were then classified as “consistent”, if detected both by VIcaller and Sung et al. “novel”, if detected by VIcaller but not by Sung et al., and “missing” if detected by Sung et al. but not VIcaller [13].