sample and variant filtering notebook

sanjaynagi / AmpSeeker

A state-of-the-art snakemake workflow for amplicon sequencing

https://sanjaynagi.github.io/AmpSeeker/

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Closed sanjaynagi closed 6 months ago

sanjaynagi commented 6 months ago

We need a processing notebook which filters out low quality variants and samples, before running the rest of the analyses. It will need to

Have sensible, general thresholds, possibly configurable in the config file.
Store an updated .bed file and metadata file with poor quality samples and variants removed.
Produce diagnostic plots which can be viewed in the result web book.

sanjaynagi commented 6 months ago

closing as duplicated with #28