To get the phased reads percentage distribution of FocalSV, you need to first run FocalSV on HG002 Hifi_L1, CLR_L1, and ONT_L1 (check our paper for data availability) using target and auto mode. For target mode, set flanking size to 50kb. Follow the instruction on our github (https://github.com/maiziezhoulab/FocalSV) to get the corresponding results.

Before running, create two folders for auto and target mode. Then under each folder, set the output to hifi_l1, clr_l1, and ont_l1 respectively.

Then run the command below.

```
plot_phased_results_combined_both.py \
--auto_dir <auto_dir> \
--target_dir <target_dir>
```