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Psy-Fer / interARTIC

InterARTIC - An interactive local web application for viral whole genome sequencing utilising the artic network pipelines..
https://psy-fer.github.io/interARTIC/
MIT License
29 stars 7 forks source link

More QC metrics on output #60

Closed Psy-Fer closed 3 years ago

Psy-Fer commented 3 years ago

Add in extra QC metrics for each sample, displayed in copy/paste compliant table, as well as add buttons to download sample as well as all samples in a tsv file.

Psy-Fer commented 3 years ago

The bulk of this is done. Needs to be reviewed.

Psy-Fer commented 3 years ago

Need to alter how variant depth is calculated. Charles at PoW raised a good point about this calculation, and how the current VCFs produced by ARTIC are.....not great. I'll do my best effort for the plots and table, as an indicator to the user, but this kind of in-depth analysis should be handled outside of InterARTIC/ARTIC as it currently is by the users we have encountered.

Psy-Fer commented 3 years ago

Okay, this is now fixed in both the QC tables and CoVar Plots.

hasindu2008 commented 3 years ago

Looks good to me! WIll close the issue for now.