Docs
How to interprete result.
Vocal output an alert level in 5 different colours which can be classified into 3 ratings.
| Alert color | Description | Impact |
|---|---|---|
| Pink | Variant is known as VOC/VOI and containing MOC or new mutations. | HIGH |
| Red | Not VOC/VOI but contain high MOC or ROI, and a new matuation (likely to cause a problem/ new dangerous). | HIGH |
| Orange | Variant contains moderately muations, or also possibly consider them either VUM or De-escalated variant. | MODERATE |
| Lila | Mostly harmless variant (near-zero mutation size for MOC or ROI). | LOW |
| Grey | No evidence of impact (either no MOC or no ROI). | LOW |
VOCAL's Knowledge base or VOCAL DB
VOCAL integrates multiple resources to construct the mutational profiles, annotate variants, and raise an alert.
Variant Status
VOCAL use a list of VOC, VOI, and VUM assignments from the ECDC, WHO and CDC. They can be accessible here.
Antibody escape mutations
We use the antibody escape scores obtained from here. All of the SARS-CoV-2 mutations assayed were in the spike protein's receptor-binding domain (RBD). The calculation score shows mutation impact to escape from antibodies. We compute the scores by summing the following escape score values obtained here: mutational_escape, site_total_escape, normalized_site_total_escape, normalized_site_mean_escape.
Parent-Child Lineage
We get lineage and sublineage relationships from Pango designation.
Lineage-defined mutation
We obtained SARS-CoV-2 mutation information for each lineage from the mutation table provided here.
Positive Selection
We use an in-house pipeline to generate positive selection information. Please get in touch with Dr. Hölzer, Martin(HoelzerM@rki.de) or Dr. Richard, Hugues (RichardH@rki.de) for more detail.
How to update VOCAL DB
We can update VOCAL database to the newest version by following two steps.
1. Update SC2 mutation information.
To update the information, we use "update.vocalDB.py" file to perform the task. We provide --online tag to download the latest files from sources.
Example commands (assume you are in the VOCAL root directory);
# To create a new annotation file.
python vocal/update.vocalDB.py sc2-mutation --online -o table_cov2_mutations_annotation.tsv
If we want to update our table_cov2_mutations_annotation.tsv, just provide the old table_cov2_mutations_annotation.tsv in -i tag.
python vocal/update.vocalDB.py sc2-mutation --online -i data/table_cov2_mutations_annotation.tsv \
--out_file table_cov2_mutations_annotation.tsv
If we want to update our table_cov2_mutations_annotation.tsv without downloading from the source (manually download NetaZuckerman_mutationsTable.xlsx from the source)
python vocal/update.vocalDB.py sc2-mutation -i data/table_cov2_mutations_annotation.tsv \
-n NetaZuckerman_mutationsTable.xlsx \
--out_file table_cov2_mutations_annotation.tsv
Then, we need to place new file under data directory
2. Update Lineages status
python vocal/update.vocalDB.py sc2-lineage-status --online -o ECDC_assigned_variants.csv \
-i data/ECDC_assigned_variants.csv -L data/lineage.all.tsv
- -L tag; sometime there are some missing lineages in the original source, so we use data/lineage.all.tsv file to help us determine the sublineages and update them. Please specify lineage.all.tsv file in the data directory to update all sublineages.
- --online tag; always download the latest information.
- -i tag; load previous ECDC_assigned_variants.csv file and update with new information.
then again we move the new file into the data directory
3. Update Lineage and Sub-Lineage information
then again we move the new file into the data directory
4. Update Positive Selection
Please contact Dr. Hölzer, Martin(HoelzerM@rki.de) or Dr. Richard, Hugues (RichardH@rki.de) for more detail.
