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Old 07-03-2011, 05:59 PM   #21
ndeshpan
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Is the IGVViewer site down?
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Old 07-03-2011, 06:43 PM   #22
Jim Robinson
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It looks like all the Broad servers were down for a short period, they are back up now. Sorry for the inconvenience.

-- Jim
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Old 07-12-2011, 10:52 AM   #23
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Hi all,

I am trying to use IGV to visualize genomic differences between yeast strains. Right now I am having trouble viewing data from just a single strain. The aligned data (using BWA) can be loaded and visualized in IGV with no problem. However, when i use samtools and bcf tools to make a pileup and then a vcf file I get an error when i try to the load the vcf file into IGV. The error says...

"Error loading features: Unable to find required field GT for the record; we don't yet support a missing GT field, at line number #### Unload track test.vcf?"

I tried loading a vcf file from the 1000 genomes project and it worked fine.

Any suggestions? FYI, I am totally new to this field so go slow.
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Old 07-12-2011, 11:00 AM   #24
Jim Robinson
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Hi,
The error message indicates that you are missing a GT field for one or more records. This field is currently required by the code we use to read VCF files (taken from the GATK). I'll update this thread when this is resolved, apologies for the inconvenience.
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Old 07-12-2011, 02:41 PM   #25
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Use "bcftools view -g" to call genotypes, which gives the GT field.
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Old 07-12-2011, 02:49 PM   #26
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That worked. Thank you both.
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Old 08-17-2011, 03:08 PM   #27
Alexander Tchourbanov
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Dear Jim,

I think the IGV is fantastic tool, thanks for developing it. I find several ways to improve the presentation. To my understanding it does not allow quick navigation by rolling the mouse and dragging the ruler. If implemented, this would be significant advantage over the existing online genome browsers, that have more static means of control. I have also found that the reference genome annotation may benefit from more colorful attributes, to delineate CDS from UTRs. An example display could be found here. Is there way to display multiple gene isoforms for human reference genome, like in case of CD44?

Thanks,

Alexander
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Old 08-17-2011, 03:42 PM   #28
Jim Robinson
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Hi Alexander,

Thank you for the suggestions. I'm afraid I don't understand exactly what you mean by "rolling the mouse and dragging the ruler". You can click and drag the view left and right as in google maps, drag the red rectangular bar, click on the cytoband, and use the keys (arrow, home end). There are also several ways to zoom. So please elaborate on specifics.

With respect to multiple isoforms, yes, right click on the track and select "Expand" or "Squished".

Best,

Jim
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Old 08-17-2011, 04:07 PM   #29
Alexander Tchourbanov
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Jim,

Thanks for quick response. Now I see how the coordinates could be changed by dragging and how isoforms could be displayed. What I meant is that central wheel on he mouse that can control the zoom on the Google maps when scrolling.

Sincerely,

Alexander
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Old 08-17-2011, 04:11 PM   #30
Jim Robinson
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Ah yes, that would be useful. But the scroll wheel is also used for scrolling vertically through tracks. Perhaps this could be a user preference.

Jim
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Old 11-02-2011, 08:49 AM   #31
CTGF
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Hi Jim,

IGV is a great tool! I use it all the time. I have a question about the “coverage”. I hope to view all the reads mapped to a region, according to IGV, the depth of the reads is about 1000. However, I am not sure whether IGV has displayed all the 1000 reads, since if I use the “expanded” view, the number of the gray bars (I assume each gray bar represents one read) doesn’t seem to be 1000. I tried the change the “Maximum read depth” under “Alignment” of the “Preferences”. However, the number of the gray bars doesn’t seem to increase. I probably missed something on the user’s manual. Thank you very much!
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Old 11-02-2011, 08:52 AM   #32
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Hi, IGV downsamples to "max read depth" for display, but counts all reads for the coverage., Changing the "max read depth" value it is the correct way to see more, you didn't miss anything. It should refresh automatically, did it seem to reload after changing the value?
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Old 11-02-2011, 10:05 AM   #33
CTGF
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Hi Jim, thanks! I closed the brower and reload the file, and now I can see all the reads.
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Old 11-02-2011, 10:57 AM   #34
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OK, thanks for reporting back. That is a bug, it should have reloaded without having to quit. I'll note it and fix it in an upcoming release.

Jim
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