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Thanks for developing this great alignment processing tool.
I would be very interested if you could add an option that would allow to filter sites/columns in an alignment based on conservation across…
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### Description of the bug
I am recently running the viralrecon 2.6.0 on some sars-cov-2 sequences; I noticed that ivar.tsv output doesn't match with the snpeff. annotated vcf as well as the varian…
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Ian has some sequences that he's aligning with MSGA. MSGA crashes on them when the MEM threader is on, but it runs through when the MEM threader is off. However, when the sequences have repetitive ele…
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Hello,
I have been using Pangolin to evaluate my tool on a simulated dataset.
However, I cannot get the lineage that I expect with pangolin. I would be glad if you could have a look why that cou…
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Transferred from sars-cov-2-variants/lineage-proposals#955
HK.3.2> C22591T> G1186T, C3425T(Orf1a:P1054S)> C27513T> G22616T(S:A352S), T25159C
Query: C21602A, T25159C, C27513T
Earliest Sequence: …
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Hi @wheaton5
I ran the souporcell_latest.sif pipeline (using singularity) successfully for 14 of my 16 libraries. In two of them I got an error and tracked back to vartrix (in the vartrix.err). Th…
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# Bug description
Running SVIM on some long read PacBio bam files, I get an error from tabix, that the resulting sequences are unsorted.
```bash
[E::hts_idx_push] Unsorted positions on sequence #1:…
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Hi,
I have used the tool to annotate and filter variants. My question is how to replace the "_" (hyphen) to the actual bases in a avinput vcf for indels from annovar converted file.
I have already…
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> And another thought: do we prevent users from using a set, where the denominator is a subset of the numerator? In that case we should have values above 1. Do we have a guard there?
_Originally po…
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The current definition of 'variant collection' in SO is “a sequence collection comprised of one or more sequences of an individual”.
A. It is not clear what is meant by ‘of an individual’ . . . this s…