What do you expect as the false positive and negative rate for SNP's and INDELS in a WGS experiment?
On which papers and data sets (inhouse or external) do you base this?
Edit: Of course this depends on a lot of thing as mentioned in the comment below. So let's assume a very vanilla situation: Human genome or popular model organism with a relative good assembly, relative close sample, maybe excluding difficult to sequence / map regions, Ilumina 100 x 100 reads, sequenced 30 x, mapped with BWA, SNP INDEL called with GATK.