Genome Trax: Variant Analysis
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Genome Trax™ is a comprehensive compilation of variant knowledge that is made available for download for easy integration into your own custom variant analysis pipeline for human whole genome, exome and targeted sequences. With Genome Trax™ content you can confidently identify known pathogenic variants or explore novel, as-yet-uncharacterized variants found within your sequence samples that are predicted to have a deleterious effect by virtue of a change in amino acid, disruption of a regulatory motif, or the disease-, drug-, or pathway-association of the affected gene.

The database includes the world’s most comprehensive collection of inherited disease causing mutations from HGMD® Professional and pharmacogenomic variants from PGMD™, as well as regulatory sites from TRANSFAC®, and disease genes, drug targets and pathways from PROTEOME™.  It integrates the best public data-sets on somatic mutations, allele frequencies and clinical variants, in their most up-to-date version, for a total of more than 165 million annotations.

Genome Trax content has been optimized to work seamlessly with ANNOVAR, an easy to use command line perl program for variant annotation that can be used by bioinformaticians to quickly set up and configure a pipeline for variant annotation. ANNOVAR™ is free for academic use and can be licensed for commercial use.

For biologists, geneticists and pathologists who want an easy-to-use interface for variant analysis, key Genome Trax™ content, including HGMD® Professional mutations, has been integrated into the Variant Analysis platform. Genome Trax™ can also be used with other software offerings including CLCbio’s Genomics Workbench and Cancer Research Workbench applications, Alamut®, Cartagenia BENCH and others.


  • Directly identify disease-causing mutations within human whole genome, exome and targeted sequences
  • Prioritize mutations from large-scale sequencing, reducing the number you have to investigate
  • Characterize novel mutations not previously reported in the literature by considering mutation effects on regulatory regions as well as the diseases, drugs and pathways linked to the affected gene
  • Predict if novel mutations are deleterious, result in protein changes or affect disease genes

Key Features

  • Directly identify relevant variants, not just filtering of common variants
  • Over 165,000,000 annotated features in total
    • HGMD® Professional disease mutations and genes
    • PGMD™ pharmacogenomic variants
    • TRANSFAC® gene regulatory elements: miRNAs, experimental transcription factor binding sites (TFBS), refined ENCODE ChIP-seq TFBS, refined ENCODE DNase hypersensitivity region TFBS, CpG islands
    • PROTEOME™ disease biomarkers, drug targets, pathway memberships
    • Up-to-date, unified access to annotation from dbSNP, COSMIC, GWAS Catalogue, ClinVar, OMIM, and other resources
  • Integrated variant effect prediction for novel variants based on machine learning, conservation, allele frequency, effect on protein sequence, and curated functional annotation
  • Fully compatible with ANNOVAR™, UCSC Genome Browser, Galaxy, CLC bio Genomics Workbench and Cancer Research Workbench, Avadis NGS, Alamut®, GeneData, Cartagenia BENCH, Microsoft Excel
  • Supports hg18/NCBI36, hg19/GRCh19 and hg38/GRCh38 reference genomes


Access Options

A download subscription provides access to all Genome Trax™ annotations in the form of .bed and .gff formatted files and MySQL relational database dump. A subset of tracks are additionally provided in VCF format. In this way, the complete Genome Trax™ data can be integrated into your own, or 3rd party, NGS analysis pipelines or tools. However redistribution of, or public access to / display of, the data is not allowed without prior written consent.

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