4. Import Genetic DataΒΆ
Genetic data comes in a myriad of custom formats and file types.
- SVS directly supports a number of file formats for several types of analysis, including Affymetrix (e.g. CEL, CHP), Illumina (Final Report, Illumina DSF), Agilent, Nimblegen, and more. All these can be found under the Import menu from the Project Navigator.
- If your genetic data is in text file you can use either Import > Text or Import > Third Party, as with pedigree and phenotype data (above). SVS will recognize genotypes as such as long as they are delimited (e.g. A_B, A/B). The delimiter can be specified during both import options. You’ll also want to specify how missing values are encoded as this can vary from file to file. Built-in missing encodings include ‘?’, and ‘—’ for each allele.
- For file formats not handled natively in SVS 7, we often write custom import scripts using SVS 7’s built-in Python scripting interface. Many of the scripts we’ve written for our customers are provided for others on our Add-on Scripts Repository For more information, or if you need help importing a custom file format, please email mailto:support@goldenhelix.com or call us at 1-888-589-4629.
Upon import you will have a spreadsheet that contains unmapped genotyped information as in Figure 5. Notice that the Map button in the upper left portion of the spreadsheet is greyed out. This will turn green once a map is applied.
Figure 5. Spreadsheet with unmapped genotype data
