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I'm not sure if this is intentional (read: I miss something that I should provide somewhere), or if this is a bug.
I tried the same thing with other SARS reads, same behavior.
### What I did:
I s…
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My own analysis of Illumina (`SRR11140750`, bottom track) and nanopore (`SRR11140751`, top track) data from the same swab sample shows your variant analysis doesn't include indels:
![image](https:/…
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*Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/322
Defining mutations: FY.3.1>G4109T (ORF1a:D1282Y)>The possible branch (Usher could not show the deletion branch?…
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## Bug Report
### Affected tool(s) or class(es)
FilterAlignmentArtifact
### Affected version(s)
Docker container running 4.1.9.0
### Description
Appears to be causing a segfault
#### S…
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Hello, my name is Andrea and I am a bioinformatician who is currently working with SARS-CoV-2 sequences in order to identify quasispecies within given samples. I have been trying to use CliqueSNV so a…
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From branch 34 of https://github.com/sars-cov-2-variants/lineage-proposals/issues/1502
KP.1.1+S:S71Y,S:S31del,
Query: A24819G, del21770_21775, del21653_21655
No of seqs: 59
First: EPI_ISL_190955…
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### Discord username (optional)
mribeirodantas
### Describe the solution you'd like?
```Text
Nextflow CLI autocomplete in Warp Terminal.
```
### Is your feature request related to a pr…
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transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/1670
KR.1 > **S:F59S** (T21738C) >> ORF1a:C3419Y (G10521A),G29543T
then>>C16675T > A13318G, T22054C (S:N164N), S:A…
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## Description
Building on the work in issue #22, output the number of cases per day, deme, and variant to support models like @marlinfiggins's Rt frequency dynamics models.
Example output looks…
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I've been through a couple of runs and the sums of the proportions of variants per sample don't sum to 1, is this correct?