igv loading genome takes forever

[Tommy Tang]

Hi all,

I downloaded IGV_2.3.5, when I loaded the genome from server, it takes forever to load.....

I am using Ubuntu 12.04.

there is no problem to load hg18 and hg19, only other genomes not showing up in the drop list.

INFO [2013-05-18 10:48:02,418]  [DirectoryManager.java:149] [main]  IGV Directory: /home/tommy/igv

INFO [2013-05-18 10:48:02,422]  [Main.java:72] [main]  Startup  IGV Version 2.3.5 (6)05/14/2013 05:23 PM

INFO [2013-05-18 10:48:02,423]  [Main.java:73] [main]  Java 1.6.0_27

Fetching user directory... INFO [2013-05-18 10:48:02,545]  [Main.java:74] [main]  Default User Directory: /home/tommy

INFO [2013-05-18 10:48:04,042]  [GenomeManager.java:117] [main]  Loading genome: http://igvdata.broadinstitute.org/genomes/hg18.genome

INFO [2013-05-18 10:48:05,742]  [GenomeManager.java:161] [main]  Genome loaded.  id= hg18

INFO [2013-05-18 10:48:05,778]  [CommandListener.java:80] [Thread-6]  Listening on port 60151

I searched and it looks like IGV 2.0 also has problem to load genome also on ubuntu.

Any ideas?

Thanks so much

Tommy

[Tommy Tang]

solved after I updated Java.

Thanks.

other problem is that after I load the bam file, nothing showed up in the track. I am using hg19 genome annotation.

I searched and found:

Q: I loaded a BAM file and don't see anything. What's wrong?

The most common cause for this is a mismatch in chromosome names between the BAM file and the IGV genome it is being viewed against.  The workaround is to create an alias file in 2-column tab-delimited format. To see how to create this alias file, see Creating a Chromosome Name Alias File in the IGV User Guide.

but the chromosome name of my bam file are chr1 chr2...etc  which should be the same as the viewing genome (hg19)

by the way, the same bam file I can load into SeqMonk without any problem.

[Jacob Silterra]

Have you tried zooming in to a location where you know there are alignments? Please post a screenshot of what you see to help us debug.

Thanks,

-Jacob

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Jacob Silterra
Software Engineer
Broad Institute

[Tommy Tang]

Thanks, I zoomed in and I saw the alignments...it looks like it needs to zoom in so much that the alignment will show up.

I used tabix to extract chr3 vcf file from ftp://ftp-mouse.sanger.ac.uk/current_indels/

and when I load into IGV (mm10),

it gave me error like this:

INFO [2013-05-20 13:06:13,524] [MessageUtils.java:60]  Error loading /home/tommy/Desktop/variants/chr3.vcf.gz: An error occurred while accessing:    /home/tommy/Desktop/variants/chr3.vcf.gz<br>Error parsing line: 3 3000011 rs261798461 TGG TG,T 106.47 GapWin;Het AC1=1;AC=30,4;AF1=1;AN=34;DP4=0,0,459,5;DP=868;INDEL;MQ=29;VDB=0.0000 GT:GQ:DP:SP:PL:FI 2/1:99:21:0:164,139,112,80,0,44:0 1/2:99:42:0:174,166,76,108,0,72:0 1/2:99:15:0:149,68,32,108,0,99:0 1/1:99:16:0:.,.,0,.,.,.:1 1/1:99:23:0:.,.,0,.,.,.:1 1/1:99:28:0:.,.,0,.,.,.:1 1/1:99:27:0:.,.,0,.,.,.:0 1/1:99:17:0:.,.,0,.,.,.:1 1/1:99:24:0:.,.,0,.,.,.:1 1/1:99:30:0:.,.,0,.,.,.:1 1/1:99:21:0:.,.,0,.,.,.:1 1/2:99:55:0:209,199,94,157,0,97:0 1/1:99:20:0:.,.,0,.,.,.:1 1/1:99:54:0:.,.,0,.,.,.:1 1/1:99:35:0:.,.,0,.,.,.:1 1/1:99:19:0:.,.,0,.,.,.:1 . 1/1:99:17:0:.,.,0,.,.,.:1, for input source: /home/tommy/Desktop/variants/chr3.vcf.gz

what's wrong with the VCF file?

[Jacob Silterra]

The fields which look like this:

1/1:99:16:0:.,.,0,.,.,.:1

should look like this:

1/1:99:16:0:.:1

IGV can handle a field which is completely missing, but if the field is a comma-delimited list then all values must be present.