Download

Latest Full Release

Version 2.0.2 (April 17, 2012)

Windows XP, Vista, 7
Mac OS X
Linux or Linux (64 bit)
Zip (Run with "java -jar Savant.jar")

Version 2.0.0 SDK (February 23, 2012)

Savant 2.0.0 SDK

Alpha and Beta Releases

Pre-release versions of Savant are made intermittently during development. They may not be entirely stable or be compatible with past versions of data or plugins.

There are no pre-release versions available at this time.

Command Line Tools (updated April 17, 2012)

The utility provides a means to format data for use with Savant from the command line.

FormatTool.sh (shell script for Mac OS X and Linux)

Source Code

You can download the latest (possibly unstable) version of Savant via SVN. Please note that this link may change in the future. Savant is licensed under the Apache License, Version 2.0. You may obtain a copy of the license here.

SVN Url: https://svn2.assembla.com/svn/savant/Savant

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Installation

Requirements

Savant is compatible with Windows, Mac, and Linux operating systems, as well as any other platform that supports JVM.
JRE 1.6 or higher

Common Issues

It is strongly recommended that you uninstall any previous version of Savant before installing a new version.
Linux users: You must first make the install file executable (by chmod'ing it).
Windows Vista/7 users: You must run the install file "As Administrator". The same goes for running the uninstaller.
If you do not have appropriate privileges to install Savant on your machine, try contacting your administrator.

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Release Notes

Version 2.0.2 (April 17, 2012)

New Features

Update SAM support to 1.4 version of spec
Support for GFF3
Popup now breaks apart GFF3 and GTF attributes.
Fetching news now honours system-wide proxy
Support for VCF3.3-style 'I' and 'D' in ALT columns
Added blue box to indicate current browsing range within variant map

Bug Fixes

NullPointerException rendering some GFF files
Block locations offset by one for BED files
GFF genes missing some blocks
Red mouseover on BAM tracks is incorrect for positions where there are insertions
Some half-paired / hanging reads not shown in arc mode
ReferenceComparator should be more robust when faced with nonstandard contig names
Popups missing on LD Plot when D' not calculated

Version 2.0.1 (March 13, 2012)

New Features

Added Frequency Mode for VCF tracks
Added option to load track from tool output upon completion
Added option to reenable zooming using the mouse wheel
Mouse wheel now works on variant map
Added legend to variant tracks
Added scrollbar so that you can continue navigating in Variant Map after "No Data in Range" message
Plugin Manager now shows descriptions and web-sites of plugins
Tool plugins are now smart enough to download required libraries

Improvements

Select arc does better job of selecting both reads
Improvements to LD plot calculation
Speeded up reading of local .fa.savant files
Min opacity for variant tracks
Widths of UCSC Explorer and tool plugins are now dynamic
Now handles VCFs with "." for missing genotypes

Bug fixes

BAMTrackRenderer is ignoring ARC_MIN threshold
Formatter not recognizing some tab delimited files
NullPointerException thrown when importing data if file-name portion exceeds 50 characters
Running GATK with a local .fa file fails because GATK looks for cached version of file
Running GATK with local hg19.fa fails with "lexicographic ordering" exception
On Linux, running GATK with remote file fails because of too many open files
Fix for sporadic 403 errors accessing files on our web-site
Names were not being displayed for generic interval track
Deletions just off the left edge of the screen were being drawn
Had problems when bookmarks had a mix of "1" and "chr1" names
Sporadic ArrayIndexOutOfBoundsException in Strand SNP mode
Data table not always updated
Very specific bug where reference is in misstep with read alignments at 41,001 - 41,101
Sporadic SQL exception using non-standard sequence files
Panning leftwards is off by one base
Insertion reported as "Deletion" in Strand SNP popup
Unable to load hg19/est using UCSC Explorer
Export of variant track from Data Table is wrong
NegativeArraySizeException opening VCF file with no participants
Variant map popups sometimes failing to appear
ArrayIndexOutOfBoundsException saving project while it is still loading
On Linux, changing the Controls does not repaint the Allele Frequency plot
Some vcf-merge files kill VCF rendering
OutOfMemoryError painting LD Plot
Selecting from a popup in the Variation module doesn't change the reference
Reads which show up in arc-mode are sometimes drawn as being mismatched against the reference

Version 2.0.0 (February 22, 2012)

New Features

Plugins
- Tool framework for wrapping external programs as plugins
- Allow plugins to add toolbars to the main navigation toolbar
- Expanded API
- Plugin for viewing chromatograms
- Rewrite UCSC plugin to provide a grid-like view of all available tracks
- UCSC Explorer should be bundled with Savant package
- IntervalTrack constructor not visible enough for plugin authors
- Allow for plugins to create BAMDataSources
- Add API for overriding track popups
- Allow plugins to refer to external jars
- Add plugin API for getting record from x,y position
- Add plugin API for using the Plugin Toolbar
- 1000 Genomes plugin needs flexibility for the root URL
Variants
- Renderer for VCF files should show participants
- Table view
- Map overview
- Allele frequency plot
- Linkage disequilibrium plot
- VCF parser should handle multiple lines for a single position
BAM tracks
- Vertical spike to indicate unpaired reads in mate pair mode
- Represent indels in SNP modes
- Add non-paired mapped as filter for BAM tracks
- Popups for SNP and Strand SNP modes
- SNP mode popup should give indication of base quality
- Select Pair should enlarge range to select both ends
- SNP and Strand SNP modes should pile up Ns
Formatting
- New file formatter for VCF files
- Allow direct use of Fasta files instead of requiring formatting
- Reporting of Tabix formatting errors could be better
- Savant should interpret standard GTF fields
- Blank lines in .GFF files should be ignored rather than causing an error
- Offer to auto-convert white-space to tabs when formatting
Projects
- Loading project should preserve track order
- Project should save Drawing Mode for open tracks
Generalised filtering mechanism (currently implemented only for BAM)
BigWigDataSource should support non-file URIs
Update 3rd-party libraries (e.g. SAM, BigWig, Tabix) to latest versions
Remove black line from insertion diamond
Should detect cache corruption and fail gracefully
Represent base quality and mapping quality as alpha values
Force .png extension on image exports
Scroll wheel should control JScrollPane, not zoom
Collision-checking on ruler labels
Eliminate showing-but-not-pinned state for Jide windows
RefSeq gene track should default to alternative name
Spruce up the start page
Add chrM to reference Fasta files
Savant should use system temp directory instead of maintaining its own
Add toggled Legends to Tracks
Make selection seem more connected to ruler

Significant Bug Fixes

Continuous tracks fail to redraw after scrolling
TDF tracks not rendering properly at very high resolutions
Caching fails if cache file grows larger than 2GB
Off by one in SNP finder
Scale to fit doesn't pack BAM reads efficiently
TDF files are not taking advantage of caching
Select Pair only works if you select second read
Arc legends are missing in 1.6.0
SNP finder throws exception when zoomed out
Odd behaviour after entering inverted range
BAM track not drawn after setting interval height to smallest size
Insertion gets overdrawn in Read Sequence mode or when Base Quality is enabled.
Gene track not always re-drawing
Not drawing rectangle when shift-dragging to select records
Undo works every other time
Ensembl gene track displays in Squish mode, but nothing in Standard mode
In 2.0.0-beta, the Table View misreports sequence data
Tools menu getting squished
Unsaved-changes marker is unreliable
Progress-bar doesn't make sense when generating coverage
Legend is empty when sequence track zoomed out
Two error messages after entering an invalid range into the location box
Old Savant icon used when minimising to dock
PluginController is downloading updates to no avail

Version 1.6.1 (October 17, 2011)

Significant Bug Fixes

Error when formatting BED files with exactly 3 columns.

Version 1.6.0 (September 22, 2011)

New Features

New piled interval view for mate pairs
Auto-completion for gene names
Handle multiple occurrences of feature name in dictionary
Thread getting data and make it possible to cancel
Add Set as Genome option to sequence tracks
Initially size the tracks according to track type
Preference to specify initial read height for BAM tracks
More control over height scaling
Add Y-axis to numeric tracks (especially useful for exporting images)
Sorting in bookmark sheet
Colours in Strand SNP mode to the axis
Export from Table View in original format (e.g. SAM/BAM for alignment tracks, tabix for tabix tracks, fasta for sequence etc.)
General framework for filtering data before being rendered
Yellow and pink arcs should be united into a single case, called "one read inverted"
Show reads in arc mode on click
New Export plugin
New Gene Ontology plugin
New Wiki Pathways plugin

Significant Bug Fixes

Prevent plugins from bringing down the UI
Progress-bar broken when downloading plugins
Known Savant genomes should remember their cytobands
SNP Finder plugin throws NullPointer exception when loading project (SNP Finder Plugin 2 calls getLayerCanvas)
Export All Selected was exporting all records (selected or not)
File repository browser should provide access to all our tracks
Plugins continue to draw after being deactivated
Colour preferences changes fail to take effect immediately
OutOfMemory errors when formatting some coverage tracks
Maximising window could break horizontal alignment of tracks

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Past Versions

Savant Genome Browser

Featured Plugin

UCSC Plugin

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Download

Latest Full Release

Version 2.0.2 (April 17, 2012)

Version 2.0.0 SDK (February 23, 2012)

Alpha and Beta Releases

Command Line Tools (updated April 17, 2012)

Source Code

Installation

Requirements

Common Issues

Release Notes

Version 2.0.2 (April 17, 2012)

New Features

Bug Fixes

Version 2.0.1 (March 13, 2012)

New Features

Improvements

Bug fixes

Version 2.0.0 (February 22, 2012)

New Features

Significant Bug Fixes

Version 1.6.1 (October 17, 2011)

Significant Bug Fixes

Version 1.6.0 (September 22, 2011)

New Features

Significant Bug Fixes

Past Versions

Version 2.0.1 (March 13, 2012)

Version 2.0.0 (February 22, 2012)

Version 1.6.1 (October 17, 2011)

Version 1.6.0 (September 22, 2011)

Version 1.5.1 (August 8, 2011)

Version 1.5.0 (June 28, 2011)

Version 1.4.4.4 (May 18, 2011)

Version 1.4.2 (December 21, 2010)

Version 1.4.1 (December 8, 2010)

Version 1.3.2.2 (October 7, 2010)

Version 1.3.2.1 (September 16, 2010)