Don't worry too much about the terminology used in different articles. In my experience the terms are often used interchangeably and also somewhat incorrectly, usually depending on the background of the person writing the article. Typically researchers are often using the term Single Nucleotide Variant now for just this reason, because we may be variant calling in different contexts and calling it a SNP would be inappropriate when we are not talking about germline variants. The term mutation is also, technically, generic, although in the human context geneticists tend to want to reserve it for deleterious variants (coming from an evolution background myself I disagree but that is a separate issue).
Without matched normal tissue (usually blood, but not always) it can be difficult to confidently determine whether a particular variant is germ line or somatic, but it depends on what you are doing as to how important this is. Tumour only sequencing is possible, and typically we use a variety of filters to try and remove as many germline mutations as possible from the dataset. Usually this is done by filtering out all mutations seen in ExAc, 1000 Genopmes, EVS, etc. It won't get everything but it will remove quite a few.
But yes, if your study or use case requires a high-confidence set of somatic only variants you would probably want to sequence either from blood (if possible) or matched normal tissue from the same individual.
modified 6 months ago
RamRS ♦ 27k
4.5 years ago by
DG ♦ 7.1k