Fig. 1

Overview of MutSpec tools and workflow. List of variants identified in a set of cancer samples may be imported as a single VCF files that contains all samples (identified by a sample ID) or as multiple VCFs (one for each sample). The first tool to use is MutSpec_Annot for annotating variants with structural and functional information. These annotations may be used to filter out variants that are known polymorphisms or located in segmental duplication regions with the MutSpec-Filter tool. If a single VCF file containing several samples is uploaded, the MutSpec-Split tool should be used to split data by sample using the sample ID. This tool generates automatically a dataset collection. If multiple VCFs are uploaded, MutSpec-Split should not be run but the annotated VCF should be grouped in a dataset collection. MutSpec-Stat can then be run on the dataset collection to generate various statistics on variants characteristics. These statistics may be visualized as graphs on html pages or downloaded as a single Excel file. The report generated by MutSpec-Stat can then be used as input of MutSpec-NMF to extract mutation signatures present in the sample set. MutSpec-NMF generates plots showing the identified signatures and the contribution of each signature to the mutation load of each sample. Finally, MutSpec-Compare can be used to calculate cosine similarity values between the obtained signatures and a set of reference signatures (published or user-defined). These results are shown as a heatmap