inconsistency between Resistance report and Resistance variants report

[alantsangmb]

Hi @jodyphelan
I noticed some inconsistency between the Resistance report and the Resistance variants report.
Specifically, for my attached result generated from v6.2.1, the pncA p.Val21Ala is listed as "Not assoc w R - Interim" in the Resistance variants report, but it is listed as Resistance in the resistance report

I have cross-checked the WHO catalogue and confirmed that this mutation is indeed "Not assoc w R - Interim" to Pyrazinamide.

Sample3576.json
Sample3576.results.zip

[jodyphelan]

It seems related to the fact that the default tbdb library comes from two sources (more on that here). It seem to be designated as not associated via the WHO catalogue but was previously reported in the literature as associated with resistance. Looking at the library there seem to be three of these cases:

Gene	Mutation	type	drug	original_mutation	confidence	source	comment
pncA	p.Val21Ala	drug_resistance	pyrazinamide	p.Val21Ala	Not assoc w R - Interim	tbdb	Mutation from literature
pncA	p.Thr160Ala	drug_resistance	pyrazinamide	p.Thr160Ala	Not assoc w R - Interim	tbdb	Mutation from literature
pncA	p.His137Arg	drug_resistance	pyrazinamide	p.His137Arg	Not assoc w R - Interim	tbdb	Mutation from literature

Some of these could potentially be conferring resistance, but perhaps the best solution here would be to remove these from the resistance list.

[alantsangmb]

Thank you so much.
What is the best way to remove these items from the resistance list?