What is the difference between Mutations and Somatic mutations Analysis?

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Mutations VS Somatic mutations

Mutations are called when aligned NGS reads suggested a minor allele different from the standard reference. Mutation analysis is conducted using Omicsoft Summarize Mutation function.

In Oncology data analysis, somatic mutations are sequence alternations occurred in tumor cells but not in matched normal cells. Only subjects with tumor-normal matched pair samples are used for somatic mutation analysis. it is calculated using Summarize Matched Pair Variation, which is based on the principle of VarScan2 [1].

In TCGA data analysis, mutation analysis was done on all samples while somatic mutation analysis was done only on matched tumor-normal subjects. Example of # data in BRCA and LUSC:

TCGAMutationDataAvailabity.png