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Transferred from https://github.com/sars-cov-2-variants/lineage-proposals/issues/656
### **Description**
**Sub-lineage of:** XBB.2.3.3
**Earliest sequence:** 2023-7-30, Netherlands, Noord-Brabant —…
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Indels-2.0 is somewhat buggy at present. On several tests it simply fails. For example the test data from https://github.com/samtools/bcftools/issues/2277.
```
bcftools: bam2bcf_iaux.c:468: iaux…
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Variants of this issue may have been mentioned in other issues, so sorry if it is a duplicate. The standard database build looks like it is trying to `overwrite 'assembly_summary.txt'` which triggers …
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In https://groups.google.com/g/hgvs-discuss/c/7I1jP5m7bvk/m/wjUzIk0zAwAJ, Matt Ducar wrote:
> ⋮
> I get the following printout:
> NC_000017.10:g.7578369A>C
>
> NM_000546.5:c.559+2T>G
>
> Th…
reece updated
5 months ago
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accumulate papers describing oligotypes and amplicon sequences and exact sequence variants
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XBB.1.5 lineage mainly found in Canada, with the rare mutation Orf6:I26V, detected in 3 other countries.
Cov-Spectrum: https://cov-spectrum.org/explore/World/AllSamples/Past3M/variants?aaMutations=…
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Hi,
Hope you are doing well. For some records in insertion variants are inconsistent with their ALT column sequences between SV_LEN.
As an example;
`1 249239182 Sniffles2.INS.5B7ES0 N GCGTCGCCTCTCT…
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Galaxy server : usegalaxy.eu
Tool version : Galaxy Version 0.1.1
(1) History which contains execution of SearchGUI+Peptide Shaker with the **comprehensive** database (reference+variants+indel+alt sp…
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Hello, My config contains the following lines:
```
GENETIC_CODE_TABLE=1
GENETIC_CODE_TABLENAME=Standard
MITO_GENETIC_CODE_TABLE=2
MITO_GENETIC_CODE_TABLENAME=Vertebrate Mitochondrial
PARENT_DI…
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Hi Shuangshuang,
Considering a gene can produce multiple transcripts, is there a method to obtain a transcript counting matrix instead of a gene-based one during data preprocessing?
Thank you!