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## Bug Report
### Affected tool(s)
HaplotypeCaller
### Affected version(s)
GATK4.beta5
### Description
HaplotypeCaller does not make some calls depending on the padding size around the in…
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**Describe the bug**
I'm working with SARS-CoV-2. I only want to incorporate indels into a variant call file with `ivar variants` and consensus genome generated with `ivar consensus` when a certain f…
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i want to see methylation values (column 11) not coverage (column 5, score) when i upload my bedMethyl file to IGV. how can i do that?
i'm following the issue with IGV and it seems everything is wor…
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Currently we're targeting java 8. As well all know, java 8 is end of life very soon and there's a question of if we want to support newer versions instead / in addition too.
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The implementation of `toString()` for annotation instances in a native image generated by SubstrateVM simply return the class name of the annotation. This breaks all uses of named or otherwise annot…
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Load 2 maps by URL. Example:
https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/primary.hic
https://hicfiles.s3.amazonaws.com/hiseq/gm12878/in-situ/replicate.hic
Zoom in to some region (maps a…
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Hi Brian,
I want to create a picture about Filtering EVM Predictions With Low Support .…
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Hello,
I've been trying ivar-1.2.3 trim, but in my hands only the first reference region of my bam file is processed (eg chr1, from a human genome) ; so in the output bam, only reads from this chom…
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I have managed to generate a minimal bam file that reproduces the issue.
First of all, you have to download the mini input.bam file from this dropbox link: https://www.dropbox.com/sh/xae79hanumpire…
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Hi,
I am using methphaser as a singularity image on an HPC. I have made the singularity image work with the test data, so shouldn't be any technical issues with the image.
I am doing adaptive se…