Varscan trio de novo mutation calling too slow

[shannjiang]

Hi,

I am using Varscan trio function to call de novo mutation. However, I found Varscan trio function is running too slow. It's unable to call per chromosome in parallel because each trio run takes a huge amount of virtual memory (approximately 50 GB). It would down the server if doing per chromosome in parallel.

Is there any better way to run varscan trio function?

Thanks,

Shan