Exome specific params?

[underbais]

Hello

Any thoughts on WES-specific filter parameters?

Thanks

[cpwardell]

Both the default settings and ICGC settings should work fine for exome data, I've used it on thousands of samples.

It's always good to have some known true and false positives in your data set that you can check are being filtered appropriately. Remember that you will always lose some true positives and keep some false positives.