Upload Files for CNV Visualization

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. NEW in 2023: We transition to new plotting methods, provided through the `bycon` package and with demonstration applications in byconaut.

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. biosample_id
   • please use only word characters, underscores, dashes
   • the sample value is used for splitting multi-sample files into their individual profiles
2. reference_name
   • 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. value
   • the value of the segment
   • should be 0-centered log2
   • 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. variant_type (optional)
   • the called type of the segment
   • one of EFO:0030067 (CN gain) or EFO:0030067 (deletion)
   • this will override a status derived from thresholding the value in mean