├── .gitignore ├── LICENSE ├── README.md ├── environment.yml ├── examples ├── H1395 │ ├── 1395_genome_copynumber.html │ └── 1395_genome_copynumber_breakpoints_test.html ├── H1954 │ ├── 1954_genome_copynumber.html │ └── 1954_genome_copynumber_breakpoints_test.html ├── H2009 │ ├── 2009_genome_copynumber.html │ └── 2009_genome_copynumber_breakpoints_test.html ├── HCC1437 │ ├── 1437_genome_copynumber.html │ └── 1437_genome_copynumber_breakpoints_test.html ├── HCC1937 │ ├── 1937_genome_copynumber.html │ └── 1937_genome_copynumber_breakpoints_test.html ├── README.md ├── colo829 │ ├── colo829_genome_copynumber.html │ └── colo829_genome_copynumber_breakpoints_test.html └── images │ ├── 1.png │ ├── 1437.png │ ├── 1937.png │ ├── 1954.png │ ├── 2.png │ ├── C15.png │ ├── C23.png │ ├── HG008_CN.png │ ├── HG008_LOH.png │ ├── copynumbers.gif │ ├── image.gif │ ├── loh1.png │ ├── loh2.png │ ├── loh3.png │ └── wakhan.png ├── requirements.txt ├── scripts └── cosmic.py ├── setup.py ├── src ├── __init__.py ├── __version__.py ├── annotations │ ├── COSMIC_cancer_genes.tsv │ ├── COSMIC_cancer_genes_nochr.tsv │ ├── chm13_genes.tsv │ ├── chm13_genes_nochr.tsv │ ├── chm13v2_cen_coord.bed │ ├── chm13v2_cen_coord_nochr.bed │ ├── grch37.cen_coord.bed │ ├── grch37.cen_coord_nochr.bed │ ├── grch37_genes.tsv │ ├── grch37_genes_nochr.tsv │ ├── grch38.cen_coord.curated.bed │ ├── grch38.cen_coord.curated_nochr.bed │ ├── grch38_genes.tsv │ ├── grch38_genes_nochr.tsv │ ├── mouse_cent.bed │ ├── mouse_cent_nochr.bed │ ├── user_input_genes_example_1.bed │ ├── user_input_genes_example_2.bed │ └── user_input_genes_example_2_nochr.bed ├── breakpoint │ ├── __init__.py │ ├── breakpoints.py │ └── breakpoints_arcs.py ├── cna │ ├── __init__.py │ ├── copynumber.py │ ├── loh.py │ ├── optimization.py │ ├── phaseblocks.py │ └── purity_ploidy.py ├── coverage │ ├── __init__.py │ ├── binning.py │ ├── processing.py │ ├── segmentation.py │ └── smoothing.py ├── file_tools │ ├── __init__.py │ ├── generate_vcf.py │ ├── process_bam.py │ ├── process_vcf.py │ └── process_vcf_legacy.py ├── hapcorrect │ ├── __init__.py │ ├── cpd.py │ ├── main_hapcorrect.py │ └── phase_correction.py ├── main.py ├── output │ ├── __init__.py │ ├── genes.py │ └── writers.py ├── plots │ ├── __init__.py │ ├── loh_hapcorrect.py │ ├── phasing_plots.py │ ├── plots_main.py │ └── snps_loh.py └── utils │ ├── __init__.py │ ├── chromosome.py │ ├── misc.py │ └── statistics.py └── wakhan.py /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KolmogorovLab/Wakhan/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/KolmogorovLab/Wakhan/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: 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