How to use FreeHiC to simulate structural variation?

[TomWang666]

Hello, I am currently using FreeHiC in my work and I would like to simulate some structural variations on GM12878. How should I set parameters to simulate multiple different types of structural variations? Looking forward to your reply！

[yezhengSTAT]

FreeHiC algorithm itself cannot create structural variations, but you can provide structural variation Hi-C matrix as a reference, and FreeHiC can simulate according to the reference map adding randomization. If you need multiple different types of structural variation, you will need to provide multiple reference contact matrices with different types of structural variation.

Hope it helps.

Thanks,
Ye