Get Started

• Introduction
• Compatible Libraries
• Workflow Requirements
• Versions
• Reference Genomes
• BaseSpace Sequence Hub User Interface Labels
• Workflow Diagram

Parameters

• Set Analysis Parameters
• Advanced Options

Analysis Methods

• Isaac Aligner
• Germline Strelka
• Manta (SV Caller)
• Canvas (CNV Caller)
• Pisces (Somatic Variant Caller)
• Picard Metrics
• PUMA Metrics
• Illumina Annotation Engine

Output

• View Analysis Output
• Analysis Info
• Log Files
• Sample Analysis Report
• Next Steps

Output Files

• BAM File Format
• VCF File Format
• Genome VCF Files
• Enrichment Summary Report
• Manifest Output File