CGAP
CGAP Improves Every Step of Case Analysis
CGAP has developed a unique end-to-end case overview
so you have access to every step of your workflow in one workspace
CGAP Improves Every Step of Case Analysis
CGAP has developed a unique end-to-end case overview
so you have access to every step of your workflow in one workspace
CGAP Improves Every Step of Case Analysis
CGAP has developed a unique end-to-end case overview
so you have access to every step of your workflow in one workspace
Upload Your Case
for Custom Analysis
• Accession Sample Data
• Ingest Family History
• Interactive Pedigrees
• Structured Phenotype & Disease Data
• Upload Sequencing Files
• WES and WGS
• Proband, Trio & Other Family Structures
• Raw Sequencing Files (VCF format coming soon)
Upload Your Case
for Custom Analysis
• Accession Sample Data
• Ingest Family History
• Interactive Pedigrees
• Structured Phenotype & Disease Data
• Upload Sequencing Files
• WES and WGS
• Proband, Trio & Other Family Structures
• Raw Sequencing Files (VCF format coming soon)
Modular Bioinformatic Pipelines Optimized for
Speed & Accuracy
• Inheritance Mode Awareness
• Optimized De Novo & Rare Variant Calling
• Quality Control Metric Dashboard
✓ FASTQ, BAM, and VCF QC analysis
✓ Sex and Ancestry Confirmation
✓ Mendelian Errors Assessment
• Provenance Graph to View Pipeline Processing
• Multisample Analysis
• SNV, InDels, SV, and CNV Analysis
Modular Bioinformatic Pipelines Optimized for
Speed & Accuracy
• Inheritance Mode Awareness
• Optimized De Novo & Rare Variant Calling
• Quality Control Metric Dashboard
✓ FASTQ, BAM, and VCF QC analysis
✓ Sex and Ancestry Confirmation
✓ Mendelian Errors Assessment
• Provenance Graph to View Pipeline Processing
• Multisample Analysis
• SNV, InDels, SV, and CNV Analysis
Integrated SNV/Indels
& CNV/SV Analysis
• Filter by Multiple Gene & Variant Properties & More
✓ Custom Gene Lists ✓ Variant Quality
✓ Inheritance Modes ✓ Variant Consequences
✓ Population Frequencies ✓ Constraint Scores
• Build Customized Filter Blocks
• Integrated SNV/Indels & CNV/SV Filtering
• Define Project Filter Presets for One-Click Filtering
Integrated SNV/Indels
& CNV/SV Analysis
• Filter by Multiple Gene & Variant Properties & More
✓ Custom Gene Lists
✓ Variant Quality
✓ Inheritance Modes
✓ Variant Consequences
✓ Population Frequencies
✓ Constraint Scores
• Build Customized Filter Blocks
• Integrated SNV/Indels & CNV/SV Filtering
• Define Project Filter Presets for One-Click Filtering
Seamless Technical Review
• Complete Technical Review & Notes on Variants
• Select Technical Reasoning for Call & No Call Decisions
• Review and Approve Decisions to Move Variants
• Save Technical Notes to your Knowledgebase
Seamless Technical Review
• Complete Technical Review & Notes on Variants
• Select Technical Reasoning for Call & No Call Decisions
• Review and Approve Decisions to Move Variants
• Save Technical Notes to your Knowledgebase
Perform Comprehensive Cohort Analysis
• Browse jointly called Whole genomes
• Explore & Assess coding & non-coding variants
• Compare gene and variant level statistics across cases and controls
Perform Comprehensive Cohort Analysis
• Browse jointly called Whole genomes
• Explore & Assess coding & non-coding variants
• Compare gene and variant level statistics across cases and controls
Explore with BAM, Annotation, Structural Variant & Cohort Browsers
• Access Detailed Annotation Space for Variant, Gene, and Sample
• Interact with Integrated CGAP Browsers for Data Visualization
• Visualize Variant Annotations in the Annotation Browser
• Review the sequencing reads in the BAM Browser
• Assess your structural variants with the SV Browser
• Quickly Navigate to SV Breakpoints
Explore with BAM, Annotation, Structural Variant & Cohort Browsers
• Access Detailed Annotation Space for Variant, Gene, and Sample
• Interact with Integrated CGAP Browsers for Data Visualization
• Visualize Variant Annotations in the Annotation Browser
• Review the sequencing reads in the BAM Browser
• Assess your structural variants with the SV Browser
• Quickly Navigate to SV Breakpoints
ACMG Interpretation & Discovery Analysis in One Place
• Add Gene & Variant Notes to Your Case
• Invoke ACMG Rules and Review Variant Classification
• Prioritize Variants and Genes for Discovery Analysis
ACMG Interpretation & Discovery Analysis in One Place
• Add Gene & Variant Notes to Your Case
• Invoke ACMG Rules and Review Variant Classification
• Prioritize Variants and Genes for Discovery Analysis
Save Your Variant Notes to Your Project Knowledge Base & Report
• Review Interpretation Notes on Genes & Variants
• Save your final Notes to Report, Project, and/or Knowledge Base
• Organize Variants by tags for your report tables
• Review your Case prior to Report Generation
Save Your Variant Notes to Your Project Knowledge Base & Report
• Review Interpretation Notes on Genes & Variants
• Save your final Notes to Report, Project, and/or Knowledge Base
• Organize Variants by tags for your report tables
• Review your Case prior to Report Generation
Customize & Deliver Informative Reports
• Summarize Your Main Findings in Custom Tables
• Present Selected Variant and Gene Interpretation Notes
• Add Custom Sections To Your Report
✓ Methodology
✓ Tested Genes
✓ References
• Add Logos and Design to Represent Your Organization/Project
Customize & Deliver Informative Reports
• Summarize Your Main Findings in Custom Tables
• Present Selected Variant and Gene Interpretation Notes & Details
• Add Custom Sections To Your Report
✓ Methodology
✓ Tested Genes
✓ References
• Choose The Logo And Design To Represent Your Organization/Project
Upload Your Case
for Custom Analysis
• Accession Sample Data
• Ingest Family History
• Interactive Pedigrees
• Structured Phenotype & Disease Data
• Upload Sequencing Files
• WES and WGS
• Proband, Trio & Other Family Structures
• Raw Sequencing Files (VCF format coming soon)
Modular Bioinformatic Pipelines Optimized for
Speed & Accuracy
• Inheritance Mode Awareness
• Optimized De Novo & Rare Variant Calling
• Quality Control Metric Dashboard
✓ FASTQ, BAM, and VCF QC analysis
✓ Sex and Ancestry Confirmation
✓ Mendelian Errors Assessment
• Provenance Graph to View Pipeline Processing
• Multisample Analysis
• SNV, InDels, SV, and CNV Analysis
Integrated SNV/Indels
& CNV/SV Analysis
• Filter by Multiple Gene & Variant Properties & More
✓ Custom Gene Lists
✓ Variant Quality
✓ Inheritance Modes
✓ Variant Consequences
✓ Population Frequencies
✓ Constraint Scores
• Build Customized Filter Blocks
• Integrated SNV/Indels & CNV/SV Filtering
• Define Project Filter Presets for One-Click Filtering
Seamless Technical Review
• Complete Technical Review & Notes on Variants
• Select Technical Reasoning for Call & No Call Decisions
• Review and Approve Decisions to Move Variants
• Save Technical Notes to your Knowledgebase
Perform Comprehensive Cohort Analysis
• Browse jointly called Whole genomes
• Explore & Assess coding & non-coding variants
• Compare gene and variant level statistics across cases and controls
Explore with BAM, Annotation, Structural Variant & Cohort Browsers
• Access Detailed Annotation Space for Variant, Gene, and Sample
• Interact with Integrated CGAP Browsers for Data Visualization
• Visualize Variant Annotations in the Annotation Browser
• Review the sequencing reads in the BAM Browser
• Assess your structural variants with the SV Browser
• Quickly Navigate to SV Breakpoints
ACMG Interpretation & Discovery Analysis in One Place
• Add Gene & Variant Notes to Your Case
• Invoke ACMG Rules and Review Variant Classification
• Prioritize Variants and Genes for Discovery Analysis
Save Your Variant Notes to Your Project Knowledge Base & Report
• Review Interpretation Notes on Genes & Variants
• Save your final Notes to Report, Project, and/or Knowledge Base
• Organize Variants by tags for your report tables
• Review your Case prior to Report Generation
Customize & Deliver Informative Reports
• Summarize Your Main Findings in Custom Tables
• Present Selected Variant and Gene Interpretation Notes
• Add Custom Sections To Your Report
✓ Methodology
✓ Tested Genes
✓ References
• Add Logos and Design to Represent Your Organization/Project