IGV 2.1.x

IGV 2.1.24 released  Sept 13, 2012.

  • Bug Fixes
    • IGV would not start on MacOS with Java 7.
    • Alignment rendering error when alignment overhangs edge of chromosome.

IGV 2.1.23 released  Sept , 2012.

  • Added support for SOCKS proxies
  • Bug Fixes
    • Error when loading VCF records with multiple allele fractions

IGV 2.1.22 released  July 20, 2012.

  • Bug Fix
    • Sample info files sometimes mistaken for GOBY alignments

IGV 2.1.21 released  July 11, 2012.

  • Bug Fix
    • Some BAM files with FZ tag will not load. 

IGV 2.1.20 released  Jun 26, 2012.

  • Bug Fix
    • Splice alignments from Goby files were occasionally not displayed.

IGV 2.1.19 released  Jun 25, 2012.

  • Updated Goby alignment file support to version 2.0.
  • Bug Fixes
    • Image snapshots from panel menus were broken.

IGV 2.1.18 released  Jun 10, 2012.

  • Added alignment "color by" option to color by both insert-size and pair-orientation anomolies.  This is now the default coloring scheme for paired-end alignments.  If a read pair has both unexpected orientation and insert-size,  the orientation color is used.
  • Change to tooltip behavior -- descriptive text is now available via a left-click on a feature when the tooltip is disabled.  The text will appear in a popup window.  Tooltips are disabled via the "balloon" icon on the command bar.
  • Bug Fixes
    • Corrupt BAM and index files could lead to infinite loop of popup error messages.
    • Alignment panel would not always repaint after a load.

IGV 2.1.17 released  May 31, 2012.

  • Bug Fix
    • VCF tooltip text was sometimes off-by-one

IGV 2.1.16 released  May 23, 2013

  • Added "setCredentials" and "clearCredentials" commands to port/batch interface.
  • Added additional tests and fallbacks for range-byte failures. 

IGV 2.1.14 released  May 16, 2012.

  • Added "logout" option to GenomeSpace menu.

IGV 2.1.13 released  May 16, 2012.

  • Bug Fix (Performance)
    • Buffer setting for loading BAM files by http was much too small, resulting in many http requests.  This could lead to poor performance on slow networks.

IGV 2.1.12 released  May 11, 2012.

  • Bug Fix
    • Column 9 attributes from GTF and GFF files was sometimes omitted from popup text.  This would occur for CDS and Exon features that did not have parent features.

IGV 2.1.11 released  May 7, 2012.

  • Added ability to create a region-of-interest comprised of a single base at the center of view by the key combination ctrl-shift-R.   This is useful to mark putative snps.   The region-of-interests can be exported as a bed file by using "Regions > Export Regions.  Note that ctrl-R defines the entire region in view as a region-of-interest.
  • Bug Fixes
    • Error when loading alignments from .bam.list file when using chromosome aliases.
    • The thickstart and thickend columns in UCSC files were sometimes ignored.
    • The locus parameter in html links was ignored.

IGV 2.1 released April 20, 2012.

  • The default location of the "igv"folder on MacOS has changed from ~/.igv to ~/igv.
  • The location of the igv folder can now be specified in on the Advanced tab of the Preferences window.  Click the "Move..." button and select a new location for the igv folder. 
  • The file used to map expression probes to genomic locations can now be specified from the Probes tab of the Preferences window.
  • A new "color" mode has been added to the alignments view in support of bisulfite sequencing experiments.
  • Specific mutations can be specified in the search box using either of the following forms:
    • [Gene name]:[reference amino acid][amino acid position][mutated amino acid]. For example, EGFR:F200L would search for a mutation from phenylalanine to leucine at the 200th amino acid position of EGFR. Only coding regions are counted
    • [Gene name]:[nucleotide position][reference nucleotide]>[mutated nucleotide]. For example, EGFR:600T>A would search for a mutation in EGFR from thymine to adenine in the 600th coding nucleotide of EGFR.
    • Single letter codes must be used in both cases. Use "*" (asterisk) for stop codon.
  • When importing a genome the sequence is no longer copied, rather the fasta file will be indexed and used in place.
  • Downsampling of alignment reads has been redesigned. Given a window size,  IGV will randomly downsample the reads who's start position fall in the window until the specified read count is reached, or the reads are exhausted.   Reading then proceeds to the next window and the sampling starts again.   Regions where reads are downsampled are marked by a small black rectangle spanning the downsampled region just under the coverage track.