I am having the same problems with two separate NextGen data. The first gives this log of errors...
ERROR [2012-11-27 17:25:45,581] [IGV.java:1493] [pool-1-thread-6] Error loading tracks
net.sf.samtools.SAMException: No index is available for this BAM file.
at net.sf.samtools.BAMFileReader.getIndex(BAMFileReader.java:199)
at net.sf.samtools.SAMFileReader.getIndex(SAMFileReader.java:268)
at org.broad.igv.sam.reader.BAMFileReader.hasIndex(BAMFileReader.java:96)
at org.broad.igv.sam.AlignmentTileLoader.hasIndex(AlignmentTileLoader.java:87)
at org.broad.igv.sam.AlignmentDataManager.hasIndex(AlignmentDataManager.java:126)
at org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:921)
at org.broad.igv.track.TrackLoader.load(TrackLoader.java:202)
at org.broad.igv.track.TrackLoader.load(TrackLoader.java:101)
at org.broad.igv.ui.IGV.load(IGV.java:1531)
at org.broad.igv.ui.IGV$10.run(IGV.java:1475)
at org.broad.igv.ui.IGV.loadResources(IGV.java:1502)
at org.broad.igv.ui.IGV$4.run(IGV.java:620)
at org.broad.igv.util.LongRunningTask.call(LongRunningTask.java:54)
at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
at java.util.concurrent.FutureTask.run(FutureTask.java:138)
at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
at java.lang.Thread.run(Thread.java:680)
INFO [2012-11-27 17:25:45,583] [MessageUtils.java:60] [pool-1-thread-6] Error loading /Volumes/HR_Passport/Work/Current Projects/AXEQ_sequence/Raw data/AXEQ_110729/MR85M100B_401.remdup.uniqMap.TS(1).bam: No index is available for this BAM file.
Not sure if this is helpful.
Thanks
Helen