Actually it was a war by proxy between Tokugawa and Toyotomi, but because of this the confrontation plot of "Iga vs. Koga" often appears in novels or ninja cartoons even today.
実際には徳川と豊臣との代理戦争だったわけであるが、今日でもよく、「伊賀対甲賀」という構図が小説や忍者漫画に出てくるのもこのためと言えよう。