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Dear,
I have two questions regarding your tool:
I used the following command: `snakemake --config markers=ucsc dataset=mypool --cores 20 --resources mem_gb=500`
1. As you can see in the log, I …
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There should be a KP.3.2/LB.1.7+C24421T sublineage that got the S2 from this LB.1.7 branch reverting S:V1104L and adding C24421T.
Interestingly it has got also a Sotrovimab known escape mutation with…
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Currently, the main page states this under Results for Genomics:
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These lists are updated daily. There are 397 sites showing intra-host variation across 33 samples (with frequencies between 5% …
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Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/488
**Potential sublineage of XBB.1.16.6 monitored by the Puerto Rico Public Health Laboratory.** [This sublineage c…
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This section includes a living Google doc form of the review on helicases as therapeutic targets, which can be viewed and edited through the following link.
https://docs.google.com/document/d/14GnyDP…
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I already mentioned this in https://github.com/andersen-lab/ivar/issues/85#issuecomment-858686771, but I am opening its own issue because I think this is a separate problem.
There is an inconsisten…
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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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Defining mutations:
KP.2 > Orf1a:P1803L (C5673T = PLPro_P240L) > C14220T > S:I934V (A24362G) > T931A, G8872A, S:N30K (T21652G)
Query: T931A,C5673T,G8872A
Samples: 7 ( 6 on Gisaid)
Countries: C…
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Inspired by @cassiawag's work on large deletions in ORF7/8 often masquerading as stretches of Ns in assemblies rather than as deletions, I had a look through currently submitted sequences to see if I …
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# Describe the bug
We have observed that ```ivar variants``` can generate false positive variant calls for SARS-CoV-2 genomes that contain insertions or deletions. Here is an example from a private…