├── CHANGELOG.md ├── LICENSE-THIRDPARTY.json ├── LICENSE.md ├── README.md ├── data ├── README.md ├── excluded_regions │ ├── cnv.excluded_regions.common_50.hg38.bed.gz │ ├── cnv.excluded_regions.common_50.hg38.bed.gz.tbi │ ├── cnv.excluded_regions.hg19.bed.gz │ ├── cnv.excluded_regions.hg19.bed.gz.tbi │ ├── cnv.excluded_regions.hg38.bed.gz │ ├── cnv.excluded_regions.hg38.bed.gz.tbi │ ├── cnv.excluded_regions.hs37d5.bed.gz │ ├── cnv.excluded_regions.hs37d5.bed.gz.tbi │ ├── convert_hg19_regions_to_hs37d5.bash │ └── get_cnv_exclusion_regions.bash └── expected_cn │ ├── expected_cn.hg19.XX.bed │ ├── expected_cn.hg19.XY.bed │ ├── expected_cn.hg38.XX.bed │ ├── expected_cn.hg38.XY.bed │ ├── expected_cn.hs37d5.XX.bed │ └── expected_cn.hs37d5.XY.bed ├── docs ├── aux_data.md ├── install.md ├── methods.md ├── outputs.md ├── performance.md ├── quickstart.md └── supporting_data │ └── Gross_2019_CNVs.csv └── img ├── hg002_chr7_tracks.png └── logo_HiFiCNV.svg /CHANGELOG.md: 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