MOVARSim presets (raw data)

This page contains the raw data, downloaded from COSMIC and TCGA, for constructing  the cancer-specific presets that inform MOVARSim simulator.

From COSMIC, we downloaded Mutation Data (Genome Screens) (https://cancer.sanger.ac.uk/cosmic/download/cosmic/v99/mutantcensus) in CSV format. Such CSV was filtered using the "PRIMARY_SITE" column to obtain one CSV file ("V99_38_MUTANT_<tumour_type>.csv") for each cancer type: “breast”, “lung”, “colon”, “adrenal_gland”, “biliary_tract”, “bone”, “cervix”, “eye”, “kidney”, “liver”, “oesophagus”, “ovary”, “pancreas”, “pleura”, “prostate”, “skin”, “soft_tissue”, “stomach”, “testis”, “thymus”, “thyroid”.

To access TCGA data, we used the GDC Data Portal (https://portal.gdc.cancer.gov/analysis_page?app=Downloads).We filtered the whole repository with the following options: - Data Category: simple nucleotide variation;- Experimental Strategy: WXS;- Data Format: maf; - Access: open.At this stage, the repository contained MAF files for various samples, each containing aggregated and filtered WES mutation calls (i.e., Tier 3 data) from different variant calling pipelines applied to tumor-normal pairs. We further filtered the repository per cancer type (PRIMARY SITE should alternatively equal “breast”, “lung”, “colon”, “adrenal gland”, “bile duct”, “bone”, “cervix”, “eye”, “kidney”, “liver”, “esophagus”, “ovary”, “pancreas”, “pleura”, “prostate”, “skin”, “soft tissue”, “stomach”, “testis”, “thymus”, “thyroid”). Finally, for each cancer type, we downloaded the MAF files corresponding to different samples and concatenated them into a single file ("merged_<tumour_type>.maf").