igv-help

Welcome to the igv-help group.  This is the official help and discussion forum for the Integrative Genomics Viewer. Please post bug reports and suggestions here. If you're having a problem, try searching this list to see if your question has already been addressed. Other resources include the  FAQ and user guide. Everyone is encouraged to contribute by suggesting bug fixes, and joining discussions of feature enhancements. 

If you are posting about a problem, please include the error message (if applicable) and your igv.log file. It will be in <your home directory>/igv. See below for further instructions on posting a bug report.

Thanks very much,
The IGV team.

When posting a bug report, please include:
  1. The version of IGV you are using
  2. What you did. If the problem happens when you open a file and/or view certain genomic coordinates, attach the file* (or provide a link) and specify the genomic coordinates.
    (e.g. I opened a bedgraph file)
  3. What you expected to happen (I expected IGV to display my data)
  4. What actually happened (I received an error message saying "Unknown extension: .graph")
*If you wish to include data, please attach a file. DO NOT paste the contents of your file into an email, as files are whitespace sensitive which gets lost when sent in the body of an email. This list does accept small attachments through email, but only using the "new" google groups view. Alternatively, use your favorite mail client to send a message to igv-help@googlegroups.com.


Showing 1-20 of 1678 topics
BUG: using relative paths to indexed fasta file as genome fails to load correctly Malcolm Cook 5:05 PM
GENE ANNOTATION MISSING Varun Gupta 8/22/16
java.lang.NullPointerException when loading saved IGV session Dan Santos 8/19/16
Sashimi plot option Rebeca 8/19/16
Re: [igv-help] not all RefSeq gene are shown in IGV Jim Robinson 8/18/16
Future release notes !!! Malcolm Cook 8/18/16
Sort/Color by tag not working for tags other than ID or SM under @RG header record Obi Griffith 8/17/16
Could not modify insertion flag threshold from alignment preferences tab. Rahim Rajwani 8/15/16
IGV preferences not working Zachary Lewis 8/14/16
Make a deduplicated TDF file Alexander Predeus 8/11/16
Make your own .genome file for IGV Alexander Predeus 8/7/16
Integrative Genomics Viewer Questions About Scaling and External Ports with Java jz...@tgen.org 8/5/16
Re: [igv-help] I am trying to convert MAF to SAM, but it runs into java error. Jim Robinson 8/5/16
Output question Jaeyun 8/4/16
IGV download visualized data TCGA Elena 8/4/16
IGV download server down? Michael Borg 8/3/16
How to register and download IGV Jennifer Nguyen 8/3/16
Downloads page now working Helga Thorvaldsdottir 8/3/16
Sequence display not working Seema Lakdawala 8/3/16
"Error encountered querying alignments: java.lang.NullPointerException" while reading bam file Paul Shannon 8/2/16
More topics »