Dear all, please could you advise :

what is the best strategy to call the somatic variants in the absence of germline sample (when only the tumor sample is available) ? thank you,

-- bogdan
If your goal is to discover new somatic variants, I am afraid that might be quite challenging because the VAST majority of variants in any sample will actually be polymorphisms and not somatic variants.  Use of a set of databases of "normal" variation to remove as many germline variants as possible can reduce the false positive results, but this approach will be clearly inferior to having a matched normal.  If, on the other hand, the goal is to identify known cancer variants present in the samples being sequenced, having tumor only is not at all unusual and is a viable strategy. 