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Currently using v2.15.3 from April 2023, v3 came out last week which might be worth bumping to
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Hi, I am trying to use pyGenomeTracks to generate a whole genome view similar to what IGV offers. However, I can only generate one plot per chromosome. Is there a way to create a whole genome preview,…
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**Description:**
We are trying to visualize the reads from SARS CoV2 samples on the gnome terminal. Upon uploading the sample file we see the following error.
> **Error encountered querying alignm…
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I want to use bamcoverage to produce some publication quality graphs with R. I got a bit puzzled how coverage is actually calculated, because it seems to be higher than what I see in IGV and also what…
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Hi,
The position of a particular variant changes when displaying it on igv.js
- Position of the variant in the gVCF and the CRAM file visualized at desktop IGV: 15-57232290-G-GA
- Position of th…
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I am going to be embedding `igv.js` in a small web application and wanted to add some browser automation tests using `playwright`.
I had a look at the markup generated by igv and while I can find t…
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I'm using new IGV version 3.0.4 with igv-webapp 2.0.0
The app seems to be trying to load the whole BAM file when loading a new track visualizing the whole chormosome.
This make the app unresponsive …
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### Description of the bug
Currently, the IGV reporting directory tries to keep all the resource files within it to make the directory self-contained. It does so through the `includeInputs` mechanism…
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Hi,
I am viewing some aligned reads on IGV as well as programmatically examining the cigar strings in my region of interest. I noticed not all the insertions/deletions present as indicated by the cig…
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**Describe the bug**
Coloring alignments by base modification removes (HP) tag grouping, and groups by strand instead.
**To Reproduce**
Steps to reproduce the behavior:
1. Go to IGV-view
2. Cl…