├── readme.md ├── version_0.9 ├── README.md ├── UPDio.pl ├── exome_designs │ └── SureSelect_v4_UPDio_input.txt ├── pre_processing │ ├── child.exome.sorted.homREFed.vcf.gz │ ├── commands_to_preprocess_files.sh │ ├── dad.exome.sorted.homREFed.vcf.gz │ └── mom.exome.sorted.homREFed.vcf.gz ├── sample_data │ ├── CNV_data_file_format_example.txt │ ├── child.exome.sorted.homREFed.vcf.gz │ ├── common_cnvs_1percent.tsv │ ├── common_variants_within_well_covered_target_regions.txt │ ├── dad.exome.sorted.homREFed.vcf.gz │ └── mom.exome.sorted.homREFed.vcf.gz └── scripts │ ├── add_hom_refs_to_vcf.pl │ ├── get_common_variants_in_target_region_file.pl │ ├── plot_zygosity_and_events.R │ ├── run_UPDio_example.sh │ ├── sort-vcf │ └── vcf_to_zygosity_plot.R └── version_1.0 ├── README.md ├── UPDio.pl ├── exome_designs └── SureSelect_v4_UPDio_input.txt ├── pre_processing ├── child.exome.sorted.homREFed.vcf.gz ├── commands_to_preprocess_files.sh ├── dad.exome.sorted.homREFed.vcf.gz └── mom.exome.sorted.homREFed.vcf.gz ├── sample_data ├── CNV_data_file_format_example.txt ├── child.exome.sorted.homREFed.vcf.gz ├── common_dels_1percent.tsv ├── common_variants_within_well_covered_target_regions.txt ├── dad.exome.sorted.homREFed.vcf.gz └── mom.exome.sorted.homREFed.vcf.gz └── scripts ├── add_hom_refs_to_vcf.pl ├── get_common_variants_in_target_region_file.pl ├── plot_zygosity_and_events.R ├── run_UPDio_example.sh ├── sort-vcf └── vcf_to_zygosity_plot.R /readme.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/findingdan/UPDio/HEAD/readme.md -------------------------------------------------------------------------------- /version_0.9/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/findingdan/UPDio/HEAD/version_0.9/README.md -------------------------------------------------------------------------------- /version_0.9/UPDio.pl: 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