🐛
📝 Describe the Issue
Genomic characterization modules that are based on static coordinates, such as SARS S gene gene_coverage, may be misapplied to incorrect coordinates in TheiaViral. Specifically, we cannot reliably link static region coordinates to dynamically selected references in genomic characterization modules. We have to identify these coordinates on-the-fly through some dynamic approach, e.g. a BLAST-based module.
We currently flag these in gene_coverage, including in TheiaCoV, with the disclaimer: "#Caution: results may be inaccurate if your sample is not mapped to the reference genome used to generate the bed file of gene locations."; it needs to be investigated if this conceptual issue extends to other characterization modules.
🔁 How to Reproduce
This is a conceptual issue dependent on if the coordinates are NOT transferable across all references in the Skani database for a specific virus - I am not aware of specific examples
The coordinate BEDfiles depicted in organism_parameters, such as sc2_gene_locations.bed, depict static gene coordinates that are not tied to a specific chromosome, which may deviate from the dynamically selected references' gene coordinates.
💻 Version Information
🐛
📝 Describe the Issue
Genomic characterization modules that are based on static coordinates, such as SARS S gene
gene_coverage, may be misapplied to incorrect coordinates in TheiaViral. Specifically, we cannot reliably link static region coordinates to dynamically selected references in genomic characterization modules. We have to identify these coordinates on-the-fly through some dynamic approach, e.g. a BLAST-based module.We currently flag these in
gene_coverage, including in TheiaCoV, with the disclaimer: "#Caution: results may be inaccurate if your sample is not mapped to the reference genome used to generate the bed file of gene locations."; it needs to be investigated if this conceptual issue extends to other characterization modules.🔁 How to Reproduce
This is a conceptual issue dependent on if the coordinates are NOT transferable across all references in the Skani database for a specific virus - I am not aware of specific examples
The coordinate BEDfiles depicted in
organism_parameters, such assc2_gene_locations.bed, depict static gene coordinates that are not tied to a specific chromosome, which may deviate from the dynamically selected references' gene coordinates.💻 Version Information