├── Makefile ├── README.md ├── SV_lengths.txt ├── SV_lengths_trans.txt ├── create_reads.py ├── docs ├── favicon.ico ├── img │ ├── Figure_comparison_paper.png │ ├── Figure_comparison_paper2.png │ ├── igv_cnvnator_del_3kb_chr21.png │ ├── igv_cnvnator_dup_40kb.png │ ├── igv_cnvnator_dup_40kb_start.png │ ├── igv_del_chrY.png │ ├── igv_longreads_dup_1kb_chrY.png │ ├── igv_longreads_inv_4kb.png │ ├── igv_pairedend_SVs_SVD_CNVn_chr20_hg38.png │ └── new.png ├── index.md ├── misc │ ├── contributing.md │ ├── credit.md │ ├── faq.md │ └── whatsnew.md └── user-guide │ ├── download.md │ ├── manual.md │ └── startup.md ├── download_and_format_database.sh ├── insert_SNVs.py ├── insert_SNVs_select_indels.py ├── insert_SVs.py ├── insert_SVs_and_indels.py ├── mkdocs.yml ├── reference ├── chrom_lengths_hg19.txt ├── chrom_lengths_hg38.txt ├── gaps_hg19.bed ├── gaps_hg19.txt ├── gaps_hg38.bed └── gaps_hg38.txt ├── simulate_SV_BED.py └── split_fasta_by_contigs.py /Makefile: 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