This repository holds scripts and raw data used by the publication:

L. Beltrame, M. Di Marino, R. Fruscio, E. Calura, B. Chapman, L. Clivio, F. Sina, C. Mele, P. Iatropoulos, T. Grassi, V. Fotia, C. Romualdi, P. Martini, M. Noris, L. Paracchini, Ilaria Craparotta, M. Petrillo, R. Milani, P. Perego, A. Ravaggi, A. Zambelli, E. Ronchetti, M. D'Incalci, and S. Marchini Profiling cancer gene mutations in longitudinal epithelial ovarian cancer biopsies by targeted next-generation sequencing: a retrospective study. Annals of Oncology, 2015.

DOI: http://dx.doi.org/10.1093/annonc/mdv164

and it is divided in several subdirectories:

• config: Includes configuration data for bcbio-nextgen
• data: Includes results (VCFs) and other data files
• programs: Includes the programs mentioned in the paper (Supplementary Section 2)

dump_counts and extract_shared_mutations require Python 2.7, while the other programs require Python 3.4.

Other dependencies:

• cruzdb
• matplotlib
• sqlalchemy
• pandas
• gemini
• sarge
• fastcluster
• numpy
• scipy
• pathlib (for Python 2.7 programs)

All programs have command-line help.

The data files included are as follows:

• all_somatic_mutations.vcf.gz: bgzipped VCF file with all the found somatic mutations
• all_somatic_mutations.vcf.gz.tbi: tabix index for the above file
• Ft-S_mutation_counts.txt: Mutation counts for Ft-S samples
• Sd-S_mutation_counts.txt: Mutation counts for Sd-S samples
• phenotype_color_table.txt: Table to use with mutation_heatmap to plot OS, PFS, and other phenotypes
• pathway_genes_and_colors.txt: Table to use with mutation_heatmap to plot the genes associated with pathways