Evoker

Evoker is a graphical tool for visualizing genotype intensity data in order to assess genotype calls as part of quality control procedures for genome-wide association studies.

It provides a solution to the computational and storage problems related to being able to work with the huge volumes of data generated by such projects by implementing a compact, binary format that allows rapid access to data, even with hundreds of thousands of observations.

[Genome Research Limited]

Downloads

Evoker is an open source project hosted on SourceForge.

SourceForge downloads

License

Copyright © 2010 James Morris & Jeffrey Barrett

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

FAQs

How do I launch Evoker for Windows?
Download Evoker from SourceForge (see 'Downloads') and unzip the install bundle then simply double click the Evoker.exe file in win folder.
How do I launch Evoker for Mac?
Download Evoker from SourceForge (see 'Downloads') and unzip the install bundle then simply double click the Evoker.app file in mac folder.
How do I launch Evoker for Unix?
Download Evoker from SourceForge (see 'Downloads') and unzip the install bundle then simply double click the Evoker.jar file in other folder.
How do I load a remote data set?
To load a remote data set select Connect to remote server from the File menu. Fill in the resulting pop-up with the following information:
  • Host is the name of the computer that the data is stored on
  • Remote directory is the absolute path of the data directory on the host machine (an easy way to get the correct string to enter in the data connection dialog for the remote directory is to login to that machine, change to that directory and run the pwd command)
  • Local directory can be any directory on the machine you are working on that you are happy to store temporary files generated by Evoker in (make sure you do not select a directory that contains important files as Evoker can delete all the files in this folder each time a new data set is loaded)
  • Username and Password should be what you use to access the remote computer
How do I generate a marker list?
An Evoker marker list is simply a plain text file containing each marker ID (the ID you use must match the ID used in the collection bim file) on a separate line.
Where will my scores be saved?
Evoker writes the scores you have recorded into a file with .scores appended to the name of the marker list you loaded.
How do I use the zoom feature?
You can zoom in and out of the plot either using the right click menu or by clicking and dragging (down and to the right creates a 'zoom in box', while up and to the left zooms back out again).
How can I identify the sample name of a point on the plot?
Holding the pointer over the point of interest will show which sample corresponds to that point.
How do I save an image of all the displayed plots?
To save a png image of all of the plots displayed in the Evoker window select Save SNP Plots from the File menu and enter your desired save location.
How can I save an image of an individual plot?
To save an image of an individual plot right click on the plot of interest and select Save as... from the menu that appears then select your save location.
What do I do if Evoker runs out of memory?
If Evoker needs more memory to load a data set then users can launch the program with additional memory from the command line by issuing the following command (increasing the -Xmx value as necessary):
java -Xmx1024m -jar Evoker.jar
Where can I find the Evoker documentation?
The evoker documentation can be downloaded from SourceForge and is also included in the download package.
How can I see the effect filtering samples has on my marker list scores?
Simply load your exclude file and the then score your marker list once with filtering turned off and once with it turned on. You must however ensure that you give each score file a different name, Evoker will warn you if you are about to overwrite a .scores file and give you the option to enter another file name.
What intensity file formats does Evoker support?
Evoker supports the following formats:
Data format Input file int2bnt.pl command line argument
Default input intensity file int2bnt.pl
Illuminus input intensity file int2bnt.pl --filetype illuminus
Chiamo (v0.1 and v0.2) input intensity file int2bnt.pl --filetype chiamo
BeagleCall allele signals file (.signals) int2bnt.pl --filetype beagle
Birdsuite allele_summary file int2bnt.pl --filetype affy
How can I connect to remote data from behind a proxy?
Users behind proxies should use an SSH tunnel to forward port 22 to another port (e.g. 2222). They can then connect to the remote machine by entering "localhost" in the host textbox and the new port in the port textbox.
How do I load more than one collection at a time, such as cases and controls?
To load multiple collections at the same time in Evoker simple requires that all the files for each collection are contained in one single directory, with each collection given a unique name. When a directory containing multiple collections is loaded Evoker will recognize the different collections and create a separate plot for each one.
Why can I not score the SNP I am viewing?
SNPs can only be scored if they are contained in a marker list that is currently loaded in Evoker.

Contact

For questions or comments, please contact James Morris or Jeff Barrett.

Publications

  • Evoker: a visualization tool for genotype intensity data.

    Morris JA, Randall JC, Maller JB and Barrett JC

    Bioinformatics (Oxford, England) 2010;26;14;1786-7

* quick link - http://q.sanger.ac.uk/2tz2hqlj