BrowseVCF 2.8

Welcome to BrowseVCF version 2.8.

NEWS/CHANGELOG: This version has a temporary file cleanup button on the Python Tk window that opens at the start. This will clean up all working files and directories within the web/tmp directory, so please use it carefully so as to not lose live working data! It also now handles "ANN" annotations from VEP.

This release contains packages for GNU/Linux, Windows, and Mac, available for download below, along with some optimisations to wormtable for handling custom data types found in some VCFs.

Please read the README.md file, which can also be found inside each package below, for detailed instructions on how to compile BrowseVCF from source (Mac and GNU/Linux) and to launch it (Windows).

We have included a tutorial PDF and a sample VCF file for testing BrowseVCF, both of which can be downloaded from the links below.

Our paper has now been published! You can find it here: BrowseVCF: a web-based application and workflow to quickly prioritize disease-causative variants in VCF files

BrowseVCF 2.7.1 (maintenance release for Windows)

This version of BrowseVCF addresses the issue of the Windows wormtable library not correctly finding its dependencies. The solution would be to install the Microsoft Visual C++ redistributables but as this is not ideal on many public machines, and as we want to maintain the portability of BrowseVCF, the wormtable library is now compiled against the static Visual Studio 2015 libraries. This also removes the need to ship vcruntime140.dll.

There are no new features, fixes, or changes to report other than this. As such, only the Windows package is provided here, as this issue currently only affects BrowseVCF on Windows. Mac and GNU/Linux users should continue use the stable 2.7 release version.

BrowseVCF 2.7

Welcome to BrowseVCF version 2.7.

NEWS/CHANGELOG: This version contains an updated Filter A with two new operators: is_present and is_absent, which allows variants to be filtered by the presence or absence of an annotated field. The Windows version also contains all fixes from version 2.6.5.

This release contains packages for GNU/Linux, Windows, and Mac, available for download below, along with some optimisations to wormtable for handling custom data types found in some VCFs.

Please read the README.md file, which can also be found inside each package below, for detailed instructions on how to compile BrowseVCF from source (Mac and GNU/Linux) and to launch it (Windows).

We have included a tutorial PDF and a sample VCF file for testing BrowseVCF, both of which can be downloaded from the links below.

Our paper has now been published! You can find it here: BrowseVCF: a web-based application and workflow to quickly prioritize disease-causative variants in VCF files

BrowseVCF 2.6.5 (maintenance release for Windows)

This version of BrowseVCF addresses an issue with the Windows wormtable package not recognising "nan" or "NaN" in VCFs. This is due to the wormtable library having been compiled with Visual Studio 2013, which changes the behaviour of the strtod() function in the C libraries.

The wormtable in this version has been compiled with Visual Studio 2015, which restores traditional behaviour in strtod.

There are no new features, fixes, or changes to report other than this. As such, only the Windows package is provided here, as this issue currently only affects BrowseVCF on Windows. Mac and GNU/Linux users should continue use the stable 2.6 release version.

BrowseVCF Pre-release UNSTABLE!

Windows only:

Attempts to fix NaN parsing issue in wormtable. Test at your own risk!

This is NOT a long-term solution. Please stay tuned for a proper release that addresses this issue comprehensively.

BrowseVCF 2.6

Welcome to BrowseVCF version 2.6.

This release contains packages for GNU/Linux, Windows, and Mac, available for download below, along with some optimisations to wormtable for handling custom data types found in some VCFs.

Please read the README.md file, which can also be found inside each package below, for detailed instructions on how to compile BrowseVCF from source (Mac and GNU/Linux) and to launch it (Windows).

We have included a tutorial PDF and a sample VCF file for testing BrowseVCF, both of which can be downloaded from the links below.

Our paper has now been published! You can find it here: BrowseVCF: a web-based application and workflow to quickly prioritize disease-causative variants in VCF files

BrowseVCF 2.5

Welcome to BrowseVCF version 2.5

This release contains many optimisations to reduce disk space usage and speed up pre-processing slightly. If a VCF cannot be pre-processed for some reason, you will now get a rudimentary error message.

Windows-specific notes

For Windows, please download the attached zip file (browseVCF_win7_vX.X.zip), unzip it somewhere, and double-click on launcher-windows.bat in the web directory. This version is shipped with a stripped-down WinPython v2.7.10, and the pre-compiled wormtable module. Tested ONLY on Windows 7.

Ships with 32-bit msvcp120.dll and msvcr120.dll (MS Visual Studio Redistributable DLLs). Also (perhaps obviously) depends on kernel32.dll but this is a system library and should not need packaging.

GNU-specific notes

You should have a Python 2.7 install along with the latest wormtable package (>= 0.1.5a2), psutil, cherrypy, and cherrypy-cgiserver. Simply navigate to the web directory on the command line and run python ./launcher-cherrypy.py.

In general, the packages should all be available via the pip tool, so it is worth installing that for the Python installation you want to use with BrowseVCF. A complete list of packages will be included in the documentation soon.

BrowseVCF 2.4

Welcome to BrowseVCF version 2.4

This release contains bug fixes to allow BrowseVCF to work with a wider variety of VCF files, especially those created on Windows.

For genotypes, "Homozygous Alt" and "Homozygous Ref" filtering are now supported.

Windows-specific notes

For Windows, please download the attached zip file (browseVCF_win7_vX.X.zip), unzip it somewhere, and double-click on launcher-windows.bat in the web directory. This version is shipped with a stripped-down WinPython v2.7.10, and the pre-compiled wormtable module. Tested ONLY on Windows 7.

Ships with 32-bit msvcp120.dll and msvcr120.dll (MS Visual Studio Redistributable DLLs). Also (perhaps obviously) depends on kernel32.dll but this is a system library and should not need packaging.

GNU-specific notes

You should have a Python 2.7 install along with the latest wormtable package (>= 0.1.5a2), cherrypy, and cherrypy-cgiserver. Simply navigate to the web directory on the command line and run python ./launcher-cherrypy.py.

BrowseVCF 2.3

Welcome to BrowseVCF version 2.3

This release contains an important bug fix. Uncompressed VCF files were not always loading correctly. This is now fixed.

Windows-specific notes

For Windows, please download the attached zip file (browseVCF_win7_vX.X.zip), unzip it somewhere, and double-click on launcher-windows.bat in the web directory. This version is shipped with a stripped-down WinPython v2.7.10, and the pre-compiled wormtable module. Tested ONLY on Windows 7.

Ships with 32-bit msvcp120.dll and msvcr120.dll (MS Visual Studio Redistributable DLLs). Also (perhaps obviously) depends on kernel32.dll but this is a system library and should not need packaging.

GNU-specific notes

You should have a Python 2.7 install along with the latest wormtable package (>= 0.1.5a2). Simply navigate to the web directory on the command line and run python ./launcher-cherrypy.py.

BrowseVCF 2.2

Welcome to BrowseVCF version 2.2

This release contains an important bug fix for Internet Explorer. Please upgrade to this version now if you are still on a previous version!

Release Notes

• Filter B (genotype) was not rendering correctly on IE due to an AngularJS issue with multiple-select boxes. The select box has been switched to nya-bs-select much like the one in step 2 to get around this problem.