VarSeq

What is VarSeq?

VarSeq is an intuitive, integrated software solution for tertiary analysis. With VarSeq you can automate your workflows and analyze variants for gene panels, exomes, and whole genomes. Understanding genomic data has never been easier thanks to our software. VarSeq software provides a powerful filtering and annotation engine to sift through large variant data sets. Using a chain of filters, you can quickly narrow your list of variants down to those that are most likely to be of interest. After determining the parameters that work well for your analysis, you can save the state of your filters so that you can easily apply the same analysis to another dataset. The same automated workflow can be used for each batch of samples, making VarSeq an ideal solution for high-throughput environments. Real-time filtering gives you the power to quickly prototype and tune analysis workflows to the specific gene panels that your lab uses. Once the appropriate set of filters have been found, the workflow can be saved and applied to future sequencing outputs without having to re-enter any parameters. After data import, annotations are automatically applied based upon your pre-configured settings. Additional annotations can then be added at any time during the analysis process. The Golden Helix team curates a wide selection of public databases and updates these datasets on a quarterly basis. The specific annotations used in your analysis are stored locally with your data and are never changed without your explicit request. This ensures that your analysis is performed on a stable dataset and your results are reproducible and available in the future. VarSeq provides coverage metrics in two forms. First, each variant displays data about the region in which it resides. This binding allows variants from suspect regions to be flagged or filtered out, which can help to prevent false positives. Second, each region in the BED file can be examined. This mode of analysis ensures that all the targeted regions were sequenced, which is crucial to preventing false negatives. 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 (frameshift, synonymous, etc.), and HGVS notation (g dot, c dot, and p dot) is provided. You can choose to filter against the highest-impact annotation for each variant or the entire set of variant-transcript interactions. Since GenomeBrowse is built into VarSeq, it is easy to verify coverage across your amplicons. Simply add your BAM and BED files to your project and inspect the pileups directly. GenomeBrowse provides the context you need to have confidence that your upstream sequencing pipeline is working correctly. Import your data, select a workflow and start exploring. It is that simple! No uploading data. No complicated parameter selection. No difficult file conversions. VarSeq distills the analysis process down to its very essence and removes all roadblocks that get in the way of getting work done.