Getting Started with Omics807

Learn how to use Omics807 for genomic analysis and somatic variant calling

Getting Started with Omics807

Welcome to Omics807, your platform for somatic variant analysis. This guide will help you understand what Omics807 is, how it works, and when to use it.

What is Omics807?

Omics807 is a revolutionary cloud-based genomic analysis platform that combines deep learning variant calling with clinical insights and comprehensive multi-omics enrichment. It transforms complex variant calling pipelines into an intuitive, visual experience accessible to researchers, clinicians, and bioinformaticians.

Key Capabilities

  • Somatic Variant Calling: Detect cancer-specific mutations in tumor samples with deep learning
  • Omics807 Insights: Comprehensive clinical interpretations with multi-omics enrichment
  • Population Genetics: Germline filtering with allele frequencies from 71,000+ genomes
  • Protein Structure Analysis: Mutation impact predictions from 200 million+ protein structures
  • Drug Target Discovery: Therapeutic matching from 1.6 million+ drug compounds
  • Pathway Analysis: Cancer pathway enrichment and protein-protein interaction networks
  • Clinical Evidence: Curated clinical evidence and research literature citations
  • Multi-Platform Support: Works with Illumina, PacBio, and Nanopore sequencing
  • Cloud Processing: Leverage your own infrastructure (Kamatera, AWS, GCP)
  • Beautiful Visualizations: Interactive dashboards and chromosome distribution charts

How Omics807 Works

Omics807 follows a streamlined pipeline to transform raw sequencing data into actionable insights:

The Omics807 Pipeline

graph LR
    A[Upload BAM Files] --> B[Transfer to Cloud Server]
    B --> C[DeepSomatic Analysis]
    C --> D[AI Interpretation]
    D --> E[Interactive Results]

Step 1: Upload Sequencing Data

  • Tumor BAM: Required - sequencing data from tumor tissue
  • Normal BAM: Optional - sequencing data from healthy tissue for comparison
  • Upload Options: Direct file upload or provide public URLs

Step 2: DeepSomatic Processing

DeepSomatic runs a 3-stage deep learning pipeline:

  1. make_examples - Creates pileup images from aligned reads
  2. call_variants - Deep neural network classifies variants
  3. postprocess_variants - Generates final VCF output

Step 3: Comprehensive Enrichment & AI Interpretation

  • Population frequency analysis for germline filtering
  • Protein structure predictions for mutation impact
  • Drug-target matching for therapeutic options
  • Pathway analysis for biological context
  • Clinical evidence from curated databases
  • Research literature citations
  • Omics807 clinical significance assessment
  • Cancer type associations
  • Recommended follow-up actions

Step 4: Results Dashboard

  • Total variants detected with enrichment scores
  • Quality metrics and filtering
  • Population genetics and protein structure analysis
  • Drug targets and therapeutic matching
  • Pathway analysis and clinical evidence
  • Chromosome distribution visualization
  • Downloadable VCF files and enriched CSV exports (50+ columns)

When to Use Omics807

Ideal Use Cases

Cancer Research - Identify somatic mutations in tumor samples - Compare tumor vs normal tissue (paired analysis) - Study mutation signatures across cancer types

Clinical Genomics - Precision medicine and treatment selection - Identify actionable mutations - Track tumor evolution over time

Method Comparison - Validate variant calling pipelines - Compare sequencing technologies - Benchmark against truth sets

Requirements

Input Files - BAM files (Binary Alignment Map) with index (.bai) - Reference genome: GRCh38 (default) - Tumor sample (required) - Normal sample (optional for tumor-only mode)

Infrastructure - Cloud server (Kamatera, AWS, GCP, etc.) - Docker support - Sufficient storage for BAM files

API Keys - SSH credentials for your server - AI service API key (for clinical interpretations)

Quick Start Example

The fastest way to test Omics807 is using the HCC1395 example dataset:

# Tumor BAM URL (chr1 region, ~100MB)
https://storage.googleapis.com/deepvariant/deepsomatic-case-studies/quick-start/S1395_WGS_ilm_tumor.bwa.dedup.chr1.quickstart.bam

# Normal BAM URL (chr1 region, ~50MB)
https://storage.googleapis.com/deepvariant/deepsomatic-case-studies/quick-start/S1395_WGS_ilm_normal.bwa.dedup.chr1.quickstart.bam

Processing Time: ~5-10 minutes for this small region

Supported Sequencing Technologies

Omics807 supports multiple sequencing platforms and workflows:

Technology Model Type Best For
Illumina WGS WGS Whole genome, high accuracy
Illumina WES WES Exome only, faster analysis
PacBio HiFi PACBIO Long reads, structural variants
Oxford Nanopore ONT_R104 Ultra-long reads
FFPE WGS FFPE_WGS Archived tissue samples
FFPE WES FFPE_WES Archived exome samples

See the Model Guide for detailed comparisons.

Understanding the Results

Omics807 provides multiple views of your data:

Summary Metrics - Total variants detected - High-quality variant count (PASS filter) - Chromosomes affected - Average quality scores

Variant Table - Position and chromosome - Reference and alternate alleles - Quality scores (QUAL, GQ, DP) - Filter status (PASS/GERMLINE/RefCall)

Omics807 Insights - Clinical significance for top variants - Associated cancer types - Treatment implications - Follow-up recommendations

Visualizations - Chromosome distribution charts - Quality score histograms - Variant type breakdown

Learn more in Understanding Results.

Next Steps

  1. Set up your server - Configure cloud infrastructure
  2. Prepare your data - Ensure BAM files are properly formatted
  3. Choose the right model - Review the Model Guide
  4. Run your first analysis - Start with the quick start dataset
  5. Interpret results - Use Omics807 insights to understand variants

Learn More

Support

Having trouble? Check our FAQ or review the technical documentation at DeepSomatic GitHub.