Introducing VariantStudio on BaseSpace

VariantStudio v2.2

Sequence and stream data to BaseSpace- done.  Run quality check- done.  Alignment and variant calling- done.  Congratulations, you now have a set of variants!  But what good is a set of variants if you can’t describe what they mean, how they might explain the phenotype of the specimen, and which ones aren’t worth worrying about? There is good news- now that Illumina VariantStudio is available on BaseSpace, deciphering the biological meaning of genomic variants is not a huge challenge.  If you’re not familiar with it, VariantStudio1 is an easy-to-use tool for variant annotation, filtering, and reporting.

  • Step 1: Import data into VariantStudio. Click the import button and you will be able to browse and select VCF and gVCF files stored in BaseSpace to import into VariantStudio.  You can import DNA variant data from targeted, exome, or whole-genome sequencing, but VariantStudio only supports human SNP and indel analysis at this time.
  • Step 2: Annotate variants using the Illumina Annotation Service, which aggregates annotations from a broad range of public sources including ClinVar, COSMIC, OMIM, and 1000 Genomes Project. Variants will be richly annotated with biological information including transcript consequence, functional impact, known disease association, population allele frequency, and more.
  • Step 3:  Apply a cascade of filtering options to quickly create a short list of candidate variants that are likely associated with the disease or phenotype. In addition to single sample analysis, you can perform tumor/normal comparisons to identify somatic mutations or family-based analyses to investigate variants underlying rare disease.
  • Step 4: Use the provided annotations to classify variants based on their presumed biological impact. A common scheme is pathogenic, likely pathogenic, benign, or unknown significance. Or you can use your own, customizable classification scheme.
  • Step 5:  Generate a customizable report that summarizes your important variants, along with any additional metadata.

Import variants > Annotate > Filter > Classify and Interpret > Generate Report.  Watch our analysis videos and see how quickly you can go through this workflow. VariantStudio is a powerful, secure2  tool to simplify genomic data interpretation, and accessing it on BaseSpace is  just a click away.  With the addition of VariantStudio to the BaseSpace Core Apps, BaseSpace users can now execute the entire sample-to-answer workflow- from generating sequence reads to reporting biologically significant results.

Related Information:

1. datasheet_illumina_variantstudio_software.pdf

2. technote_variantstudio_data_security.pdf



  1. Nice application. Very fast, with remarkable flexibility. Two comments.

    It would be helpful to make more explicit the distinction between fields computed from the sample date, and those which are pulled from other population-based datasources. For example, drilling into the help file was required to find that the number reported as “allelic freq” is not computed, but pulled from all populations of 1000 genomes data; April 2012 phase 1 call set (v3 update).

    And there appears to be a bug in the Genotype field. I see several examples of high quality insertions, 4 to 20 bases in length, with only 24 to 40% variant frequencies (based on sample read depth), called “homozygous”. These look heterozygous to me.

    • Thanks for your comments, GGAnderson. Your suggestion to distinguish fields computed from the sample data from annotation sources is a great one. Perhaps this can be achieved through simple color coding of the column headers, or indicated through the tooltip when hovering over the column headers.

      Regarding the potential bug in the Genotype field, VariantStudio simply reads that information in from the GT field of the uploaded VCF file; it does not generate that information itself. With the files that we’ve tested, this parsing is done correctly in VariantStudio. It would be of great help if you can send a VCF file with the example you described to our tech support team ( so that we can investigate further.

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