├── .gitignore ├── Dockerfile ├── LICENSE ├── README.md ├── data ├── data_hg19.zip └── data_hg38.zip ├── example_config.hg19.yml ├── example_config.hg38.yml ├── indelible.py ├── indelible ├── __init__.py ├── __init__.pyc ├── __pycache__ │ ├── __init__.cpython-36.pyc │ ├── aggregate_positions.cpython-36.pyc │ ├── annotate.cpython-33.pyc │ ├── annotate.cpython-36.pyc │ ├── blast.cpython-36.pyc │ ├── fetch_reads.cpython-36.pyc │ ├── indelible_lib.cpython-36.pyc │ ├── score_positions.cpython-36.pyc │ └── trio_caller.cpython-36.pyc ├── aggregate_positions.py ├── aggregate_positions.pyc ├── annotate.py ├── annotate.pyc ├── blast.py ├── blast.pyc ├── blast_repeats.py ├── build_database.py ├── bwa_runner.py ├── coverage_calculator.py ├── fetch_reads.py ├── fetch_reads.pyc ├── forest_trainer.py ├── indelible_lib.py ├── indelible_lib.pyc ├── score_positions.py ├── score_positions.pyc ├── trio_caller.py └── trio_caller.pyc ├── requirements.txt ├── test_data ├── DDD_MAIN5194229_Xchrom_subset_sorted.bam ├── DDD_MAIN5194229_Xchrom_subset_sorted.bam.bai ├── DDD_MAIN5194229_Xchrom_subset_sorted.bam.indelible.tsv ├── DDD_MAIN5194229_Xchrom_subset_sorted.hg38.bam └── DDD_MAIN5194229_Xchrom_subset_sorted.hg38.bam.bai └── vr_runner_scripts └── run-indelible /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HurlesGroupSanger/indelible/HEAD/.gitignore -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HurlesGroupSanger/indelible/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/HurlesGroupSanger/indelible/HEAD/LICENSE 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