Data Management

Need to Import a Custom File Format?

Recognizing that data formats are constantly evolving, we often write Python scripts to import custom data formats. Many are provided in our in our script repository. If you cannot find what you need, let us know and we'll see if we can help.

Script Repository | Request Custom Script

Supported File Formats

Numerous file formats are supported directly or via custom Python scripts.

• Affymetrix
  SVS 7 is an Affymetrix GeneChip-compatible application, meaning it can directly import data from mos Affymetrix GeneChip Human Mapping Arrays (including 5.0 & 6.0) as well as the Cyto 2.7M and Molecular Inversion Probe (MIP) arrays. You can also use the integrated NetAffx service to download the most up-to-date Affymetrix marker maps and library files.
• Illumina
  Custom report plug-ins are available for Illumina’s BeadStudio and GenomeStudio programs streamlining the export of Illumina genotype and copy number data to the Golden Helix DSF format. Download Illumina Import Plug-ins ››
• Progeny Lab
  Progeny Lab includes an option to create a custom query, export genotype and phenotype data to the Golden Helix DSF format and launch an SVS 7 project with a click of a button.
• Agilent
  A new Agilent import tool reads Agilent text files (TXT tab delimited files) created with the Agilent Feature Extraction software.
• Nimblegen
  Direct import of Nimblegen Data Summary Files is now supported.
• Third Party Formats
  Numerous third party formats are supported including ASCII (.txt, .csv), Excel, Ped/Bed, SAS, SPSS, Strata, Matlab, and more.
• Import Scripts
  Aware that an unlimited number of custom file formats exist, each requiring special parameters, we often write custom Python scripts to properly import custom data formats. Included are HapMap, Illumina final report, and Parallele long file import scripts. If you need a custom script written to get your data into the software please contact us and we will be glad to help.

Supported Data Types

SVS 7 supports a wide range of data formats supporting population-based case-control, quantitative trait loci (QTL), and categorical type analysis. Dependent variables can be binary and continuous. Supported predictors include binary, continuous, ordinal, categorical, nominal and genetic (bi- and multi-allelic genotypes, microsatellites, etc.) variables.

Integration of Genomic Annotations

Seeing is believing with an intuitive interface that puts your data in genomic context at every step. Discover how rewarding it is to navigate whole genome data live within a spreadsheet - complete with genomic annotations - or visually in a genome browser. For follow up analyses you can quickly look up significant markers in supported online databases. More consistent workflows make performing complex analyses quick, easy, and efficient.

Project Navigation

In accordance with sound laboratory practices, a project navigator automatically time-stamps and logs each analysis step and provides efficient means for tracking and annotating results. You can also share project files with colleagues, which is particularly helpful when collaborating on projects.

Sparse Data Storage Technology

All data is stored in a sparse storage format enabling you to rapidly import large-scale whole-genome data, analyze it with conventional hardware, and efficiently share projects among collaborators. Your entire genome-wide association study (GWAS) study can fit on a single USB Flash drive!