Upload Files for CNV Visualization

CNV Data Plotting

Here we provide users an option to visualize their own CNV data, using the standard Progenetix plotting options for histograms and samples. This functionality is currently limited to single segmens files without the group labeling options. However, we provide the plotting libraries as a Perl package through our Github repository.

Drag and drop some files here, or click to select files.

Segment File format

NEW 2021: We now recommend the use of our .pgxseg file format for th eupload of CNV segments files. As an extension of the standard tab-delimited segment file format below, the .pgxseg file format allows the addition of e.g. group label information. The file format is described on our documentation site, including link to an example file.

Otherwise, data has to be submitted as tab-delimited .tsv segment files. An example file is being provided here.

While the header values are not being interpreted (i.e. it doesn not matter if the column is labeled referenceName or chro), the column order has to be respected:

  1. sample
    • please use only word characters, underscores, dashes
    • the sample value is used for splitting multi-sample files into their individual profiles
  2. referenceName
    • the reference chromosome
    • 1-22, X, Y (23 => X; 24 => Y)
  3. start
    • base positions according to the used reference genome
  4. end
    • as above
  5. mean
    • the value of the segment
    • 0-centered
    • segments not passing the calling thresholds (fallback 0.15, -0.15) are being filtered out
    • one can use dummy values (e.g. 1 for gains, -1 for losses)
  6. probes (optional)
    • the number of array probes, call bins in the segment
    • fallback filter removes
    • optional (no filter on empty values)
  7. variant_type (optional)
    • the called type of the segment
    • one of DUP or DEL
    • this will override a status derived from thresholding the value in mean