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PoonLab / gromstole

Quantifying SARS-CoV-2 VoCs from NGS data of wastewater samples
MIT License
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Maintain a local database of mutation frequencies from gromstole outputs #88

Open ArtPoon opened 9 months ago

ArtPoon commented 9 months ago

The resulting database would be enormous, though. It might be more efficient to just use grep across outputs.

ArtPoon commented 9 months ago

First steps would be to investigate how feasible this would be to build and maintain

ArtPoon commented 6 months ago

Omit rows from *.mapped.csv inputs where the mutation was observed in one read only, i.e., frequency * coverage = 1. This will exclude roughly one-fifth of rows from the database

ArtPoon commented 6 months ago

The script populating the database died on Paphlagon

ArtPoon commented 5 months ago

Please refer to collate_mapped.py and aggregate_mapped.py regarding target outputs