greve Genomic Recurrent Event ViEwer 

GREVE: Genomic Recurrent Event ViEwer to assist the identification of patterns across individual cancer samples.
Cazier J-B, Holmes C, Broxholme J.(2012), Bioinformatics. doi: 10.1093/bioinformatics/bts547, Free Online Access.

Select a DataSet to Plot

Mini Demo Demo Data File
In doubt, select Mini_Demo, and push the Submit button

Select Optional files to upload

Configuration file
Gene file
Give your own configuration file if you want to modify the default layout of the summary
Give a gene list if you want to highlight them in the chromosome view

Select Optional Title

This will appear on top of each figure.
By default the input file name will be used.

Select Filters to Apply

Select Chromosomes

Chrom 1 Chrom 2 Chrom 3 Chrom 4 Chrom 5 Chrom 6 Chrom 7 Chrom 8
Chrom 9 Chrom 10 Chrom 11 Chrom 12 Chrom 13 Chrom 14 Chrom 15 Chrom 16
Chrom 17 Chrom 18 Chrom 19 Chrom 20 Chrom 21 Chrom 22 Chrom X Chrom Y
Genome-Wide Summary   All chromosomes

Information on Plot

Overlap and Events   Show Overlap details   Show by individual Show Score
Overlap only, no Events   Collapse Events in summary   Highlight LOH Show GW Poisson-Binomial
Events only, no Overlap   Show Cytoband names   Plot Profile Show Chr. Poisson Binomial
      Include DGV events. DGV filter:    


build 35 (hg17)     build 36 (hg18)     build 37 (hg19)

Output Image Format

Tagged Image File Format (TIFF)     Portable Document Format (PDF)     Portable Network Graphics (PNG)


  1. Description
  2. Gallery
  3. Parameters
  4. Command-line version
  5. F.A.Q.
  6. Recent changes.
  7. To do.

1. Description

This interface to the GREVE software generates plots and summary from your own list of events, typically Copy Number Variations (CNVs), and genes.
It normally takes a list of events and plot them genome-wide, or per chromosome, in the context of cytoband and/or genes. It is designed to be highly configurable to allow both on-line exploration as well as pulbication-ready figures in various format. One key feature is the characterisation, and plotting, of overlapping regions of a given type of Events.

Try the demo files or have a look at some published work using this site to get a better idea:

This map shows how much GREVE is being used all over the world !

2. Gallery

Genome-Wide view per Type Genome-Wide view per Individual
Chromosome view per Type with overlaps and genes Chromosome view per Individual with genes
Genome-view of the scores per type, Manhattan style

3. Parameters


Plot Data
Graphically depicts complete data for selected chromosomes. Can be filtered by Chromosome, Type of Events, cytoband name and overlap.
Table File
Beware this can take few minutes with larger array.
Note: The file should be TAB delimited with following header and unlimited number of rows:
PatientID Chr Type Start End Comment
A few sample datasets are available: Note: This file will take about a minute to process

Gene File
The gene file contains information about genes to be plotted in the chromosome view.
It shall contain information about the gene location and name with a header containing the following fields:
Name Chr Start End
Note that the file has to be in text format

Configuration File
The Configuration file contains some parameters to run the program: Sections are defined between square brackets, '[]', and comments start with '#' or ','
A demonstration configuration file is available


Select Chromosomes:

Select a specific chromosome number or all the chromosomes at once by selecting "Genome-Wide Summary"

Select visible parameters:

Information on Plot
Select whether you want to see some particular information on the plot
Overlap of Events:
Show the overlap of a specific Event type
Collapse Events in summary:
Allow identical events across samples to be merged in summary.
Details can be modiofied with the configuration file.
Cytoband Name:
Show the name of the cytoband inside the chromosome if possible
Show by individuals:
The Events are presented by a fixed set of individuals, with overlapping events.
Currently only implemented for the genome-wide view
Highlight LOH:
If the string "LOH" is found in the event name, then this section will contain extra highlighting.
Suggest to set the same color for the event with and without LOH with the Configuration file.
Known CNV from the Database of Genomic Variants can by included in the plot.
Because of the diversity of source for this resource it is possible to add a filter for a given pulication and/or Author:
The filter works as an AND operator of ":" separated fields. For example Affymetrix:Conrad will provide all variants found with Affymetrix platform AND found in Conrad et al.
Plot Profile:
Show the selected score on the chromsome and new summary view
Show Score:
Show the Score in the above profile
Show GW Poisson-Bionomial:
Show the Genome-Wide Poisson-Bionomial in the above profile
Show Chr. Poisson-Bionomial:
Show the Chromosome-Wide Poisson-Bionomial in the above profile


Three builds are available to match the events to the cytobands: Build35 (hg17), Build36 (hg18) and Build37 (hg19).
DGV references will be set automatically according to these three builds. Build 37 is the default.

Output Image Format

Five possible output formats are available for the plots:
By default Encapsulated PostScript (EPS) and are provided JPG (images shown). But it is possible to generate TIFF, PDF and PNG format as well.
Beware that the more format generated the longer it will take to process.


Multiple output are possible depending on the chosen parameters:


Per chromosome

For each chromosome there are essentially two type of output:

log files

Both Standard Output and Standard Error from the Python command are available for inspection.
These should help investigating potential reason for failure to process as expected.

4. Command line version

This page propose a convenient graphical interface to a Python based software.

However, the Python engine is available directly to allow batch runs as well as very specific tailoring.
To install GREVE on your own machine you will need the following pieces:

Do not hesitate to contact the author to share some extension of yours.

5. F.A.Q.

Nothing is showing. What is going on?
You need to make sure that you follow the 2 possible formats described above: TAB separated text file, Excel file.
Furthermore make sure you filename contains only 1 ".".
If you use Excel format, make sure it is 97-2004 format, rather than the latest.
Finally make sure that you have setup enough colors in the configuration file for the number of event type you are using.

Processing is slow. Is it normal?
Depending on the size of your input file, and the action required, the process can take few minutes.
You might want to skip the costly verlap definition, reduce the number of file type generated, or the number of chromosomes analysed.

I do not like to color choice. Can I modify it ?
Yes. The choice of color is made in the order of the type found in your list.
You can modify it by giving your own configuration file, selection your own color in Red-Green-Blue (RGB) code.

My bars go over to the next chromosome. Can I change this behaviour?
Yes. First I would recommend to tick the "Collapse Event in summary" box to put together recurrent events.
Furthermore, the respective position of the chromosome, the size of the bari, the distance between bars are all configurable.
You can modify it by giving your own configuration file.

There are a lot of overlap on the centromeres and telemores. Is this real?
Unlikely. There is little information in terms of markers in those regions and their recurrent calling is probably an artefact of the data and calling method.
It is recommended to filter the list of CNV before submitting them to GREVE.

Can I avoid sorting my event and see the Events per individual?
Yes. There is an option to plot the Events per individual rather than per event (--ind). In this case the order of the input file is kept across all chromosomes.

Why is the indivual plot not showing on the chromosome level?
Currently only the Genome-View has got the individual plot implemented. The chromosome is in the ToDos list.

My gene list does not seem to be loaded or shown. Is this feature not working?
The gene list is limited to about 50,000 features because of PHP restictions.
This should be sufficient for gene illustration, especially with the names showing. It is however possible to include more features by using the command line directly.

I cannot see the LOH events despite checking the box. What is happening?
LOH is represented by a thin line around the normal box. Because of the various formats it can be difficult to see on the screen (jpeg).
However it should be clearly visible in the EPS and PNG formats.

What is the Poisson Binomial test?
The Poisson Binomial uses the proportion of each individual carrying a given event, genome-wide and chromosome-wide, to test how likely it is they overlap N times.
If the probabilities for each individual were equal, it would correspond to the usual Binomial distribution.

Which score should I use?
There are 4 scores reported for each segment of each type. They can be classified into 2 subgroups:

Is GREVE used at all beyond the author?
Yes, the Geomap shows the usage around the world, turning into many known publications

The GUI is great, but I'd like to run it myself. Is there a command line version?
Yes this is essentially a web interface to a python based software. You can find the details above

Whaoo this tool is fantastic !!! Is it published?
Yes. It has been accepted for publication by Bioinformatics

My question is not part of the FAQ. How shall I do?
Please contact the author who will be delighted to attempt solving your problem

6. Recent Changes.

7. Still To Do.

  1. Add pair testing to the web-version rather than just hard-coded.
  2. Create a version for non-human CNV (in process through collaboration)
  3. Allow for newer Excel format by replacing the xlrd package
  4. Make Circos plot for the summary.
  5. Allow parameters on the Configuration filei, such as bar thickness, to be modified on the main page.

Last updated on November 2012

Please contact Jean-Baptiste Cazier for details