├── .editorconfig ├── .gitattributes ├── .gitignore ├── CADD.sh ├── CHANGELOG.md ├── Dockerfile ├── LICENSE ├── README.md ├── Snakefile ├── config ├── config_GRCh37_v1.6.yml ├── config_GRCh37_v1.6_noanno.yml ├── config_GRCh37_v1.7.yml ├── config_GRCh37_v1.7_noanno.yml ├── config_GRCh38_v1.6.yml ├── config_GRCh38_v1.6_noanno.yml ├── config_GRCh38_v1.7.yml ├── config_GRCh38_v1.7_noanno.yml ├── impute_GRCh37_v1.6.cfg ├── impute_GRCh37_v1.7.cfg ├── impute_GRCh38_v1.6.cfg ├── impute_GRCh38_v1.7.cfg ├── references_GRCh37_v1.6.cfg ├── references_GRCh37_v1.7.cfg ├── references_GRCh38_v1.6.cfg └── references_GRCh38_v1.7.cfg ├── data ├── annotations │ └── .gitignore ├── models │ ├── GRCh37 │ │ ├── CADDv1.6-GRCh37.mod │ │ ├── CADDv1.7-GRCh37.mod │ │ ├── LICENSE │ │ ├── conversionTable_CADDv1.6-GRCh37.txt │ │ └── conversionTable_CADDv1.7-GRCh37.txt │ └── GRCh38 │ │ ├── CADDv1.6-GRCh38.mod │ │ ├── CADDv1.7-GRCh38.mod │ │ ├── LICENSE │ │ ├── conversionTable_CADDv1.6-GRCh38.txt │ │ └── conversionTable_CADDv1.7-GRCh38.txt └── prescored │ ├── GRCh37_v1.7 │ ├── incl_anno │ │ └── .gitignore │ └── no_anno │ │ └── .gitignore │ └── GRCh38_v1.7 │ ├── incl_anno │ └── .gitignore │ └── no_anno │ └── .gitignore ├── envs ├── environment_minimal.yml ├── esm.yml ├── mmsplice.yml ├── regulatorySequence.yml └── vep.yml ├── install.sh ├── schemas └── config_schema.yaml ├── src └── scripts │ ├── VCF2vepVCF.py │ ├── annotateVEPvcf.py │ ├── appendPHREDscore.py │ ├── extract_scored.py │ ├── lib │ ├── AnalysisLib.py │ ├── Annotations.py │ ├── EDict.py │ ├── __init__.py │ ├── columnInfo.py │ ├── tools │ │ ├── MMSplice.py │ │ ├── esmScore │ │ │ ├── __init__.py │ │ │ ├── esmScore_frameshift_av.py │ │ │ ├── esmScore_inFrame_av.py │ │ │ ├── esmScore_missense_av_fast.py │ │ │ └── esm_lib.py │ │ └── regulatorySequence │ │ │ └── predictVariants.py │ └── tracks.py │ ├── max_line_hierarchy.py │ ├── predictSKmodel.py │ └── trackTransformation.py └── test ├── input.vcf ├── input.vcf.gz ├── 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