high throughput next generation sequencing is a powerful tool to identify the genotypic landscapes of somatic variants and therapeutic targets in various cancers including gastric cancer forming the basis for personalized medicine in the clinical setting although the advent of many computational algorithms leads to higher accuracy in somatic variant calling no standard method exists due to the limitations of each method here we constructed a new pipeline we combined two different somatic variant callers with different algorithms strelka and varscan 2 and evaluated performance using whole exome sequencing data obtained from 19 japanese cases with gastric cancer gc then we characterized these tumors based on identified driver molecular alterations more single nucleotide variants snvs and small insertions deletions were detected by strelka and varscan 2 respectively snvs detected by both tools showed higher accuracy for estimating somatic variants compared with those detected by only one of the two tools and accurately showed the mutation signature and mutations of driver genes reported for gc our combinatorial pipeline may have an advantage in detection of somatic mutations in gc and may be useful for further genomic characterization of japanese patients with gc to improve the efficacy of gc treatments j med invest 64 233 240 august 2017.