Analyzing PacBio Data with SNP & Variation Suite

         March 21, 2012

As most in the Golden Helix community are aware, SNP & Variation Suite (SVS) can handle all sorts of data including files from Affymetrix, Illumina, Agilent, and Complete Genomics with its powerful data management capabilities. Announced in February, SVS is now part of the Pacific Biosciences Partner Program and has the ability to analyze PacBio files.

In this short, five minute video, Gabe Rudy, Vice President of Product Development, demonstrates analyzing PacBio data using SVS. The workflow includes:

  1. Importing PacBio data after converting to VCF file format.
  2. Selecting a default genome built for visualization and analysis.
  3. Joining phenotypic information with genotype data.
  4. Viewing matching variants with the NHLBI 5400 Exome Sequencing Project.
  5. Filtering variants using the dbSNP 135 Dataset of Common Variants.
  6. Using the SVS genome browser to compare filtered and unfiltered data and gaining additional information using annotation tracks.

Similar analysis steps can, of course, be followed for any other NGS data. …And that’s my 2 SNPs.

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