Detection of Oncogenic and Clinically Actionable Mutations in Cancer Genomes Critically Depends on Variant Calling Tools

The analysis of cancer genomes provides fundamental information about its aetiology, the processes driving cell transformation or potential treatments. While researchers and clinicians are often only interested in the identification of oncogenic mutations, actionable variants or mutational signatures, the first crucial step in the analysis of any tumor genome is the identification of somatic variants in cancer cells (i.e. those that have been acquired during their evolution). For that purpose, a wide range of computational tools have been developed in recent years to detect somatic mutations in sequencing data from tumors. While there have been some efforts to benchmark somatic variant calling tools and strategies, the extent to which variant calling decisions impact the results of downstream analyses of tumor genomes remains unknown. Here we present a study to elucidate whether different variant callers (MuSE, MuTect2, SomaticSniper, VarScan2) and strategies to combine them (Consensus and Union) lead to different results in three important analyses of cancer genomics data: identification of cancer driver genes, quantification of mutational signatures and detection of clinically actionable variants. To this end, we tested how the results of these three analyses varied depending on the somatic mutation caller or strategy in five different projects from The Cancer Genome Atlas (TCGA). Our results show that variant calling decisions have a significant impact on these analyses, creating important differences that could even impact treatment decisions for some patients.  Moreover, the Consensus calling strategy to combine the output of multiple variant calling tools, a very widely used strategy by the research community, can lead to the loss of some cancer driver genes and actionable mutations. On the other hand, the Union seems to be a legit strategy for some downstream analyses with a robust performance. Overall, our results point to important differences in critical analyses of tumor sequencing data depending on variant calling and highlight the limitations of widespread practices within the cancer genomics community.