Using build GRCh37 (hg19)  Overview | Multiple | Upload Data | Family Info

Run Analysis

Some information

Choose the method to use above, and follow instructions on those pages.

The standard method is multiple algorithm analysis. When you choose this method, you will get the following results:

  • - Bookmark files to import into BeadStudio / GenomeStudio for the combined results and the seperate algorithms.
  • - A graphical overview of the project, plotting all called aberrations against genomic positions, control panels, known genes and Decipher entries.
  • - For each called CNV you will can get a zoomed in plot for detailed analysis.
  • - For each sample a PDF is created containing LogR and BAF plots per chromosome, with indication of the called CNVs
  • - QC-values generated by PennCNV are stored and can be reported.
  • - Per sample detail pages, listing all called CNV's, positions, disrupted genes and occurence frequencies.

When seperate algorithms are run, you will only be presented with a bookmark file that can be imported into BeadStudio/GenomeStudio. These XML's can also be processed into tabular format listing CNV positions, disrupted genes and some other basic info on a per sample basis.

Input Format Converter

While it is very easy to extract data in the correct format from BeadStudio, it can be rather hard to reformat 'Full Call Reports' into the correct format. I have create three simple scripts to convert these files into the correct format (only tested on a linux machine). It can be downloaded here: Download