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Hi, I've noticed some discrepancies in the delly.vcf output file and what is displayed in IGV.
I've loaded .bam and .vcf to IGV. When I scroll to see the variants I see such picture:
, if files are included in the scout config?
Currently Nallo out…
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Hi there:
I called SNPs using freebayes and got 2 SNPs (15725855 and 15726131) but the variant is now shown in IGV, is my process wrong or sth else?
This occurred to other sample with depth more tha…
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# Summary
Users cannot view reads. The IGV panel opens, but the tracks do not load. Inspecting the browser console reveals that an HTTP request for reference files returns with a 403 error.
The HT…
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Unexpected error: Cannot invok
"org.broad.igv.feature.Cromosome.getLength(）" because "Chr" is null
See igv.log for more details
igv.log
[LongRunningTask] Exception running task
SEVERE [11月 13,2…
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Hi,
How can I further validate called Structural Variants (SVs) besides using IGV, especially when the number of SV variants may be in the hundreds or even thousands? Could you give me some ideas?
…
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Loading the hs1 genome using the 3.0.7 pre-built fails with this error:
IGV-Web app version 2.0.6
igv.js …
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Hi, I’m asking why the total count of IGV differs from the total count of bam-readcount.
As you can see the total count on IGV is 8827+9462=18289, while the total count with bam-readcount is 182…
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Hi, I see some differences in how variants look when VCF vs gVCF are explored in IGV.
See example in the attached screenshot, positions look exactly in the actual record but index looks different …
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Recently upgraded IGV from 2.17.4 to 2.18.4. With this update, we noticed that IGV session made with whole transcriptome bam files, would not load correctly.
They would load initially, but any sub…