├── .github ├── ISSUE_TEMPLATE │ ├── feature-request.md │ └── report-issue.md ├── PULL_REQUEST_TEMPLATE.md └── workflows │ ├── add-issues-to-project.yml │ └── style.yaml ├── .gitignore ├── Dockerfile ├── README.md ├── data ├── cancer-predisposition-genes.txt ├── clinvar_all_disease_concept_ids.txt ├── clinvar_cpg_concept_ids.txt ├── output_colnames_default.tsv ├── test_VEP.hg38_multianno.txt.intervar ├── test_VEP.vcf ├── test_VEP.vcf.hg38_multianno.txt ├── test_VEP_final_081123.vcf ├── test_autopvs1.txt ├── test_final_081123.hg38_multianno.txt ├── test_final_081123.hg38_multianno.txt.intervar ├── test_final_081123_autopvs1.txt ├── test_pbta.autopvs1.tsv ├── test_pbta.hg38_multianno.txt ├── test_pbta.hg38_multianno.txt.intervar └── test_pbta.single.vqsr.filtered.vep_105.vcf ├── docs └── release-notes.md ├── figures └── germline-pathogenecity_flow.png ├── results └── .gitignore ├── run_autogvp.sh └── scripts ├── 01-filter_vcf.sh ├── 02-annotate_variants_CAVATICA_input.R ├── 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