├── CNV_overlap.py ├── CNV_read_depth_checker.sh ├── CNVnator.py ├── CNVworkflowlib.py ├── COMMANDS.sh ├── Canvas.py ├── ERDS.py ├── Genome_STRiP.py ├── IQR_samtools_depth.py ├── IQR_samtools_depth.sh ├── LICENSE ├── LUMPY.py ├── MANTA.py ├── RDXplorer.py ├── README.md ├── SV.py ├── VCF.py ├── add_features.py ├── benchmark_overlap_counts.py ├── cnMOPS.py ├── compare_CNVs_to_benchmark.py ├── compare_with_RLCR_definition.py ├── convert_CNV_calls_to_common_format.py ├── format_cnvnator_results.py ├── format_erds_results.py ├── functions.py ├── get_normalized_depth.py ├── hg19_gap.bed ├── index_samtools_depth.py ├── merge_Genome_STRiP.py ├── merge_cnvnator_results.py ├── merge_erds_results.py ├── myvcf.py ├── process_cnvs.erds+.sh ├── reproduce_results.sh └── split_HuRef_benchmark.sh /CNV_overlap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bjtrost/TCAG-WGS-CNV-workflow/HEAD/CNV_overlap.py 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