├── .gitignore ├── ExomeTableClean.R ├── Homo_sapiens.GRCh37.87.genes.bed.gz ├── Homo_sapiens.GRCh37.87.genes.bed.gz.tbi ├── LICENSE ├── README.md ├── UCSC_wholegenes.bed.gz ├── UCSC_wholegenes.bed.gz.tbi ├── WESdiag_pipeline_dev.sh ├── WESdiag_pipeline_dev.sh_bkup ├── assess_variants.sh ├── clinvar_anno.R ├── clinvar_prep.sh ├── clinvar_variant_summary_filtered_url.RDS ├── clinvar_variant_summary_filtered_url.txt.gz ├── configuration.sh ├── coverage_stats └── .blank ├── diagnostics_exome_reporting.Rproj ├── example_logFile.log ├── gene_lists └── .blank ├── images ├── Pipeline_flowchart_v2.pdf ├── Pipeline_flowchart_v2.png ├── Pipeline_flowchart_v2.tiff ├── ShinyDallianceViewer_nozoom.png ├── ShinyDallianceViewer_zoom.png ├── ShinyFilterTool_screenshot.png ├── VariantAnno_tool_page.png └── image_process.sh ├── report ├── .Rhistory ├── GRC_report_v0.1.3.Rmd ├── GRC_wes_pipeline_guide.pdf └── template │ ├── GRC Diagnostics Clinic Genotyping Analysis Report - Prototype_v2_10.02.16.docx │ └── GRC_WES_report_template_landscape.docx ├── results ├── Tier_0 │ └── clean │ │ └── .blank ├── Tier_1 │ └── clean │ │ └── .blank ├── Tier_2 │ └── clean │ │ └── .blank ├── Tier_3 │ └── clean │ │ └── .blank ├── Tier_4 │ └── clean │ │ └── .blank └── mutation_links │ └── .blank ├── server.R ├── server.R_bkup ├── ui.R ├── vcf └── .blank ├── vcfcompiler_diagnostics.sh ├── wes_reporting.R └── wes_vcffiltering.sh /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sirselim/diagnostics_exome_reporting/HEAD/.gitignore -------------------------------------------------------------------------------- /ExomeTableClean.R: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/sirselim/diagnostics_exome_reporting/HEAD/ExomeTableClean.R -------------------------------------------------------------------------------- /Homo_sapiens.GRCh37.87.genes.bed.gz: 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