├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── annotate_windows.sh ├── calc_coverage_from_bam.sh ├── calc_window_mappability.py ├── call_cnv.c ├── data ├── clamms_special_regions.grch38.bed ├── clamms_special_regions.hg19.bed └── example_qcs.Rdata ├── fit_models.c ├── hmm.c ├── hmm.h ├── ltqnorm.c ├── normalize_coverage.c ├── plot_cnv.R ├── plot_cnv.sh ├── sam_gatk_coverage_to_bed.c ├── split_targets_into_windows.awk ├── transpose.gawk ├── utils.c └── utils.h /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rgcgithub/clamms/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/rgcgithub/clamms/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: 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