Comments (5)
RaverJay
commented on July 4, 2024
1
Should be. On it
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replikation
commented on July 4, 2024
oh its a separate column for this?. would make sense just to add it to the other ones. maybe with a highlight
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hoelzer
commented on July 4, 2024
Yep, seems so. Need to check the nextclade (srry I think I meant nextclade not nextstrain) output, but might be easy to grep and add
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RaverJay
commented on July 4, 2024
Do you mean the aaDeletions column?
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hoelzer
commented on July 4, 2024
Do you mean the aaDeletions column?
This was actually a user request and I think pangolin is not reporting INDELs, or? So the idea would be to grep them from Nextstrain. For example, for B.1.1.7 there should be del69/70 and Y144del in the Spike. The deletions are super important for immune/ test escape and thus it would be of high value to have them in the report.
And yes, I imagine that information is in the aaDeletions column?
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Related Issues (20)
- Pangolin v4.0 HOT 11
- Include artic-tools "validate_scheme" HOT 1
- Runs fail at barcode22 HOT 8
- Private mutation from nextclade HOT 1
- Frameshift correction
- "split-fasta"-process fails due to leading empty line
- Workflow failed at artic_medaka, no '2.Genomes' output, with test_fastq and actual sample HOT 1
- export variant file (vcf) HOT 1
- add skip scorpio parameter to pangolin HOT 1
- Only calculate NanoPlot after read filtering step HOT 5
- Add new V5 ARTIC primer BED HOT 5
- Medaka step fails in the -profile fastq_test HOT 3
- summary_report.py fails HOT 7
- publish primersitereport from medaka output
- VarSkipV2b primer does not work as expected HOT 7
- Update Medaka to support R10.4.1 models HOT 14
- Update --help to list up-to-date primer schemes that are supported
- MinKNOW/Guppy update needs new model for R10.4.1 5 kHz HOT 6
- Warning when execution report and timeline already exists HOT 1
- The pipeline fails in artic_ncov_wf_artic_medaka HOT 7
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