In this rare-variant association study for hepatocellular carcinoma (HCC), 280 HCC patients were recruited by our groups, and were subjected to WES. To avoid erroneous variants detection, we performed variants calling for all the samples simultaneously. All samples were individually called using Haplotype Caller of The Genome Analysis Toolkit (GATK v3.6) according to GATK best practice pipeline, and jointly called using GenotypeVCFs with default settings, respectively. After strict quality controls, we retained 268 samples for downstream analysis.