├── LICENSE ├── Makefile ├── README.md ├── Snakefile ├── config └── cluster.json ├── data └── example │ └── patients │ ├── patient1 │ └── sample1 │ │ ├── segments.tsv │ │ ├── somatic_indels.vcf │ │ ├── somatic_snvs.vcf │ │ └── somatic_sv.tsv │ ├── patient2 │ └── sample1 │ │ ├── segments.tsv │ │ ├── somatic_indels.vcf │ │ ├── somatic_snvs.vcf │ │ └── somatic_sv.tsv │ └── patient3 │ └── sample1 │ ├── segments.tsv │ ├── somatic_indels.vcf │ ├── somatic_snvs.vcf │ └── somatic_sv.tsv ├── examples └── example │ ├── patient1 │ └── sample1 │ │ ├── cnv.txt │ │ ├── indel.vcf │ │ ├── snv.vcf │ │ └── sv.tsv │ ├── patient2 │ └── sample1 │ │ ├── cnv.txt │ │ ├── indel.vcf │ │ ├── snv.vcf │ │ └── sv.tsv │ └── patient3 │ └── sample1 │ ├── cnv.txt │ ├── indel.vcf │ ├── snv.vcf │ └── sv.tsv ├── output └── example │ ├── cohorts │ └── all │ │ └── hrdetect │ │ ├── hrdetect_input_table.tsv │ │ ├── hrdetect_input_table_paths.tsv │ │ └── hrdetect_output_table.tsv │ └── patients │ ├── patient1 │ └── sample1 │ │ ├── hrd_scores │ │ └── hrd_score.tsv │ │ ├── hrdetect_components.tsv │ │ ├── indel_microhomology │ │ ├── indels_annotated.tsv │ │ └── microhomology_scores.tsv │ │ ├── snv_signatures │ │ ├── mutation_catalog.tsv │ │ ├── signit_exposure_summary.tsv │ │ ├── signit_exposure_summary_fractions.tsv │ │ └── signit_output.Rds │ │ └── sv_signatures │ │ ├── sv_catalog.tsv │ │ ├── sv_signit_exposure_summary.tsv │ │ ├── sv_signit_exposure_summary_fractions.tsv │ │ └── sv_signit_output.Rds │ ├── patient2 │ └── sample1 │ │ ├── hrd_scores │ │ └── hrd_score.tsv │ │ ├── hrdetect_components.tsv │ │ ├── indel_microhomology │ │ ├── indels_annotated.tsv │ │ └── microhomology_scores.tsv │ │ ├── snv_signatures │ │ ├── mutation_catalog.tsv │ │ ├── signit_exposure_summary.tsv │ │ ├── signit_exposure_summary_fractions.tsv │ │ └── signit_output.Rds │ │ └── sv_signatures │ │ ├── sv_catalog.tsv │ │ ├── sv_signit_exposure_summary.tsv │ │ ├── sv_signit_exposure_summary_fractions.tsv │ │ └── sv_signit_output.Rds │ └── patient3 │ └── sample1 │ ├── hrd_scores │ └── hrd_score.tsv │ ├── hrdetect_components.tsv │ ├── indel_microhomology │ ├── indels_annotated.tsv │ └── microhomology_scores.tsv │ ├── snv_signatures │ ├── mutation_catalog.tsv │ ├── signit_exposure_summary.tsv │ ├── signit_exposure_summary_fractions.tsv │ └── signit_output.Rds │ └── sv_signatures │ ├── sv_catalog.tsv │ ├── sv_signit_exposure_summary.tsv │ ├── sv_signit_exposure_summary_fractions.tsv │ └── sv_signit_output.Rds ├── projects ├── compass.smk ├── example.smk └── pog.smk └── scripts ├── basic-functions └── row_bind_tables.R ├── hrdetect ├── aggregate_scores.R ├── compute_hrdetect.R └── hrdetect_input_table.R ├── hrdscore └── run_test.R ├── microhomology ├── compute_microhomology_scores.R └── flank_indels.R ├── projects ├── compass │ ├── format_segments.R │ ├── format_sv.R │ └── vcf_to_snv_indel.R └── pog │ └── merge_delly_abyss.R ├── signatures ├── get_mutation_catalog.R ├── signit_exposures.R └── signit_summary_table.R └── sv 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