search

BIMSBbioinfo / pigx_sars-cov-2

PiGx SARS-CoV-2 wastewater sequencing pipeline
GNU General Public License v3.0
18 stars 3 forks source link

variant_report: merge mutation frequencies when they contribute to the same aa freq #70

Closed vicfabienne closed 2 years ago

vicfabienne commented 3 years ago

image (13)

Description

When multiple genomic mutations lead to the same AA mutation, they are listed as separate mutations. This leads to breakage when generating the csvs for the plots but also to wrong deconvolution results.

What's need to be done?

In this case the affected rows would have to be merged with adding up the frequency values in the 3ed column. This would have to be performed on this "complete.df".

vicfabienne commented 3 years ago

debug_completeDF.csv

This is the complete.df from the sample where this bug is from. Maybe hepls when debugging

vicfabienne commented 3 years ago

fixed on "WIP_fix_issue#70"

vicfabienne commented 2 years ago

we changed from working with aa mutations to only work with NT mutations. They will only be translated to aa mutations for reporting and summary purposes. With this, this issue is not a problem anymore