This work presents a digital hardware design to accelerate the HaplotypeCaller in the Variant Discovery phase of Genome Analysis Tool-Kit (GATK), which is a software toolkit for genetic sequencing data analyzing. We implement and redesign HaplotypeCaller by using a software-hardware co-design environment composed of C++ and Verilog, and program the hardware part on an FPGA board. The overall performance of our software and hardware co-design platform achieved a speed-up of 6.2 times, compared to the software counterpart of GATK.