Table 1 A comparison of the FPGA and CPU implementation of variant calling of the NA12878 data.
From: Improving read alignment through the generation of alternative reference via iterative strategy
Method | Variant type | FP | FN | TP | Precision | Sensitivity | Time (min) | Memory (GB) |
|---|---|---|---|---|---|---|---|---|
GTX-One | InDel | 8711 | 15,999 | 464,578 | 0.9816 | 0.9667 | 33 | 33.2 |
SNP | 14,706 | 20,601 | 3,188,714 | 0.9954 | 0.9936 | |||
GBP | InDel | 6339 | 11,312 | 469,265 | 0.9867 | 0.9765 | 1904 | 30 |
SNP | 9312 | 31,760 | 3,177,555 | 0.9971 | 0.9901 |
