├── Dockerfile ├── LICENSE ├── README.md ├── config.params ├── data ├── PRED_DIR │ └── README.md ├── VALD_DIR │ └── README.md ├── bp_coverage_dir │ └── README.md ├── canoes │ └── .gitkeep ├── clamms │ └── .gitkeep ├── codex │ └── .gitkeep ├── cons_calls.bed └── xhmm │ └── .gitkeep ├── prechecks.sh ├── scripts ├── calc_valdata_overlap.sh ├── calculate_CNV_overlap.sh ├── canoes_call_CNVs.sh ├── canoes_extract.sh ├── clamms_extract.sh ├── clamms_postprocess.sh ├── clamms_preprocess.sh ├── cn_learn.py ├── cn_learn.sh ├── codex_extract.sh ├── codex_postprocess.sh ├── extract_bp_coverage.sh ├── extract_gc_map_vals.sh ├── merge_overlapping_CNVs_endjoin.sh ├── merge_overlapping_CNVs_readdepth.sh ├── research │ └── plots_for_paper.r ├── rscripts │ ├── CANOES.R │ ├── canoes_merge_files.r │ ├── codex.r │ ├── consolidate_val_ov.r │ ├── generate_interval_combo.r │ ├── identify_targets_of_interest.r │ ├── measure_rd_stats.r │ ├── merge_init_preds.r │ └── reshape_caller_overlap_data.r ├── xhmm_call_CNVs.sh └── xhmm_extract.sh ├── software ├── bigWigAverageOverBed ├── bigWigToWig ├── clamms.tar.gz ├── gatk-3.5.tar.gz ├── libpng12-0_1.2.54_amd64.deb └── xhmm.tar.gz └── source ├── R-3.4.4.tar.gz ├── dummy.bed ├── sample_list.txt ├── sample_list_test.txt ├── sample_list_train.txt └── targets_auto_no_chr.bed /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/girirajanlab/CN_Learn/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/girirajanlab/CN_Learn/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/girirajanlab/CN_Learn/HEAD/README.md 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