VarSeq ® software eases the burden of discovering high impact variants in NGS datasets. Large whole exome or whole genome datasets can be analyzed on your local machine. Annotations are automatically applied based upon your pre-configured settings and additional annotations can be used at any time during the analysis process. VarSeq enables filtering based on inheritence patterns, affection status, and arbitrary sample groupings.
Phenotype Based Gene Ranking
Variants can be prioritized by examining how closely the mutated gene is related to the patient's phenotype. By examining biomedical ontologies that link diseases with genes, the algorithm can rank genes according to the proband's phenotype. These generated rankings can be combined with traditional filtering techniques to quickly surface candidate variants.
Powerful Variant Annotation
Included in VarSeq is functionality similar to SnpEff or Variant Effect Predictor. Each variant is mapped to all overlapping transcripts and information about the region where it is located (exon, intron, intergenic, etc.), sequence ontology (frame shift, synonymous, etc.), and HGVS notation (g dot, c dot, and p dot) is provided. Additional statistics, such as distance from coding start, distance from exon boundary, and the number of codons changed make it easy to examine specific classes of variants.
Inheritance and Affection Status Based Filtering
VarSeq includes first-class support for workflows that use pedigree, affection status, or custom groupings to define filter criteria. Prebuilt filters are available for most common inheritance patterns. Custom filters can be easily created using family information. Additionally, affection status alone can be used to construct useful segregation analysis of complex family pedigrees to find candidate regions and variants.
Inheritance Based Filters:
- Autosomal dominant
- Autosomal recessive
- De novo
- Compound Heterozygous
- Custom inheritance based filters (e.g. Maternal Heterozygous, etc.)
Powerful Visualization Built In
All the power of GenomeBrowse is built into VarSeq. Using your BAM files, GenomeBrowse allows you to quickly verify that the variant matching your criteria isn't an artifact of the sequencer or upstream algorithms. Additionally, it allows you to answer any questions that might remain about the genomic context of a variant. Is the variant near an intron boundary? Are there common mutations nearby? Does the reference sequence have issues in this region? Are there other variants in the sample in-phase with this one? By being tightly integrated into VarSeq, GenomeBrowse can visualize the same data sources used to annotate your variants. Say goodbye to tedious file and protocol management and see your data in a whole new way.
Case Study - Chaim Jalas, Bonei Olam
Finding Rare Mutations at the Center for Rare Jewish Genetic Disorders
Webcast - Improve Variant Analysis Research Workflows
Blog Post - Whole Exome Sequencing workflows
A look at whole exome sequencing workflows in VarSeq and SVS.
eBook - Clinical NGS Analysis
Our latest 2nd edition copy!
By Dr. Andreas Scherer