I'm using Scalpel (version "0.4.1 (beta)") and want to use it for normal/tumor calling.
I'm using it with the recommended parameters from the manual. When exporting the somatic variants, the resulting VCF file only has one sample column (for the somatic events only).
Is there a way to make Scalpel write out the results for the normal sample as well, similar to MuTect? This way, I could look at the properties of the calls in the matched normal sample for comparison with the tumor call.