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
Are you looking for sensitive identification of all somatic variants, particular actionable variants (eg gene fusion breakpoints), or signs of large-scale events such as chromothripsis?

If you're happy to control your FDR by accepting a low sensitivity and ignoring small to medium sized indelsthen it's viable as I demonstrated [here][1]. If you're interesting in TE reactivation then you're going to need a normal as it's practically impossible to determine if those events are germline or not.

  [1]: https://rd.springer.com/chapter/10.1007/978-3-319-42044-8_27