New Tutorial: VarSeq CNV Caller

The new VarSeq CNV Caller Tutorial covers the basics of the VarSeq CNV calling algorithm, with an emphasis on visualization and interpretation of results.

Figure 1. New CNV Caller Tutorial

This workflow requires an active VarSeq license with the CNV Caller on Target Regions feature included. You can go to Discover VarSeq or email info@goldenhelix.com to request an evaluation license with the CNV functionality included.

The VarSeq CNV calling algorithm relies on coverage information computed from BAM files. The algorithm uses changes in coverage relative to a collection of reference samples as evidence of CNV events. Using these reference samples, the algorithm computes two evidence metrics: Z-score and Ratio. The Z-score measures the number of standard deviations from the reference sample mean, while the Ratio is the normalized mean for the sample of interest divided by the average normalized mean for the reference samples.

Figure 2. Example of a Heterozygous Deletion

The tutorial will walk you through the following:

  • Running the CNV Caller Algorithm
  • Performing Sample Quality Control
  • Plotting CNV Results
  • Interpretation of some example calls

If you have any comments or questions about this new tutorial please let us know!

Additional VarSeq tutorials and resources can be found here.

About Jami Bartole

Jami Bartole came aboard Golden Helix in 2012 and is currently our Senior Field Application Scientist. Prior to that, Jami worked at the University of Montana – Helena College as a Mathematics Instructor and at the Montana Department of Justice as a Quality Assurance Auditor. Jami completed her Masters in Mathematics from Montana State University – Bozeman and her BS in Mathematics from Montana Tech – Butte. In her free time, Jami enjoys reading and spending time with her friends and family.

2 thoughts on “New Tutorial: VarSeq CNV Caller

  1. Michele Ramsay

    Dear Jami,
    I am writing because we are using SVS 8.4.4. and are not clear about the notation for variant calling specifically the following classes:
    Synonymous
    Non-Synonymous
    Substitution (A substitution that does not cause a frameshift – no substitution case frameshifts unless they affect splicing – or have I got this wrong?)

    The help file is not helping.

    Synonymous = substitution
    Non-Synonymous = substitution
    Substitution = either synonymous or non-synonymous, if coding.

    Please assist.

    Reply
    1. Jami Bartole

      Hi Michele,

      For the Variant Classification tool that is found in SVS 8.4.4 the annotations are defined as follows: Synonymous is a variant affecting one or more nucleotides that does not change the amino acid sequence; Non-synonymous is a single nucleotide variant that changes the amino acid produced by the codon. Both are considered coding substitutions. Frameshifts are substitutions that cause a shift in the codon reading frames. Full documentation on the annotations for protein coding variants can be found in the SVS manual at the following link.
      http://doc.goldenhelix.com/SVS/8.4.4/svsmanual/variant_classification.html#protein-coding-variants

      In the most recent version of SVS (8.7.0) we implemented a new Transcript Annotation algorithm so the annotation results will now be defined using the naming convention defined by The Sequence Ontology Project. You can find specifics on the new tool in our manual at the following link.
      http://doc.goldenhelix.com/SVS/latest/svsmanual/sequencing_analysis.html#annotate-variant-effect-on-transcripts

      If you have further questions feel free to email me at support@goldenhelix.com.

      Thanks,
      Jami….

      Reply

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