WGAViewer

Version history

WGAViewer is being continuously developed by Drs. Dongliang Ge and David Goldstein at Duke Institute for Genome Sciences & Policy, Center for Human Genome Variation.

** Version histoty **

#1.25G
A function to load imputation results is implemented. (Menu: File -> Load imputation results)
#1.25H
Critical update: functions to check the closest gene are updated to comply with the latest updates of the Ensembl databases.
#1.25I
New updates:
Supporting some European languages that use decimal (",") instead of point (".") for decimal symbol;
Ignoring blank lines in input files (in previous version the loading will stop at blank lines);
Pilot functions to support copy number variation output from PennCNV software (Wang et al. http://www.neurogenome.org/cnv/penncnv/).
#1.25J
New updates:
- A bug causing confusion in top hits cutoff settings is fixed.
[Top hits annotation function]: in the previous versions, when p-val cutoff is selected and "top N" is set to zero, a warning
will be incorrectly issued.
#1.25K
New updates:
- A bug causing problem in displaying annotation results for SNP list without GWAS results is fixed.
[Tools -> Annotate a list of SNPs]: in the previous versions, the comprehensive annotation results for a list of SNPs without GWAS results
cannot be displayed unless WGAViewer is restarted.
#1.25L
New updates:
- A new format of annotation project file (binary .wga file) is implemented. This new format with a hard-disk buffering feature will allow a more
efficient top-hits annotation. The previous formats are supported as well.
- Supporting multiple gene links for complex transcripts.
- Supporting multiple genomic location hits for certain genes, especially for micro RNAs. Previous versions will annotate from the smallest possible
genomic locations to the largest, which will cause annotation problems in some cases.
- Supporting multiple genomic location hits for certain SNPs. Previous versions will expand the annotation region to the smallest possible genomic locations
to the largest, which will cause LD calculation difficulty in some cases.
- A function to detect abnormal termination of the program and to clean up temporary data files is now implemented.
- A previous bug in displaying weblink in LINUX platform is now fixed.
#1.25M
New updates:
- A bug is fixed: in version 1.25M the function "Tools -> Annotate a list of SNPs" won't enable annotation project file so the annotation cannot proceed.
#1.25N
New updates:
- A bug is fixed: 1,25N users cannot annotate top hits through proxy server. This is due to a recent update in Duke proxy and now is fixed. Users with direct connection are not affected.
#1.25O
New updates: some cosmetic updates.
#1.25P
New updates:
- A bug is fixed: 1.25M/N/O/P users cannot load reference database. This is due to a bug in updating the software. It is now fixed in 1.25Q.
#1.25Q
New updates:
- A new function is added: Multiple rawcnv files (for example in different phenotypic groups) now can be loaded together. This function is useful in inspecting
CNVs in different phenotypic groups, for example, in cases and controls separately.
#1.25R
New updates:
- Cosmetic updates to include more information if annotation were not complete.
- A new function is added: Creating smaller subset for users with limited memory (RAM) resources. This new function ("Tools->Other tools->Create a subset") enables users to create a smaller dataset based on a P value criterion. Loading this smaller dataset will require much less RAM.
#1.25S
New updates:
- Allows an additional (conf) column in RAWCNV file.
#1.25T
New updates:
- A bug is fixed: versions prior to 1.25U will halt while annotating unplaced (unmapped) SNPs using "Tools -> annotate a list of SNPs" function, but annotating top hits won't be affected. It is fixed in this version 1.25U.
[*IMPORTANT NOTE*]: this updated version 1.25U and later versions will no longer support the binary .wga file created by earlier versions, including the example dataset released with the earlier versions.
To download the updated .wga example dataset suitable for version 1.25U and later, visit:
http://igm.cumc.columbia.edu/WGAViewer/downloadexample.php
Flat text .wr file is not affected.
- Some other cosmetic updates.
#1.25U
New updates:
- A bug is fixed: versions prior to 1.25V will not display reference data after a full annotation.
[*IMPORTANT NOTE*]: this updated version 1.25U and later versions will no longer support the binary .wga file created by earlier versions, including the example dataset released with the earlier versions.
To download the updated .wga example dataset suitable for version 1.25U and later, visit:
http://igm.cumc.columbia.edu/WGAViewer/downloadexample.php
Flat text .wr file is not affected.
#1.25V
New updates:
- A tool is added: [Tools->Other tools->Merge text files]. This tool simply append one text file at the end of the other.
#1.25W
New updates:
- A bug is fixed: when overwriting project file, versions prior to 1.25X will incorrectly buffer annotation files.
This will throw an 'annotation file missing' exception. Saving project as another file is not affected.
- Some cosmetic updates.

** ----------------- **

This project is supported by the Center for HIV-AIDS Vaccine Immunology (CHAVI, http://www.chavi.org/) and the Duke Institute for Genome Sciences & Policy (IGSP, http://www.genome.duke.edu/).

For questions and comments send the author an email: Dongliang Ge, PhD d.ge@duke.edu