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jodyphelan / TBProfiler

Profiling tool for Mycobacterium tuberculosis to detect ressistance and strain type from WGS data
GNU General Public License v3.0
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Unreported deletion in pncA gene #343

Open insapathogenomics opened 5 months ago

insapathogenomics commented 5 months ago

Hello,

I have a MTB strain with a large deletion in pncA gene, that should leed to LoF. In a previous version of tb-profiler this deletion reported resistance to Pyrazinamide (as well as in the current online version), while now it apears in the "Other variants report" (Position 2277353).

See output attached. Ran with default settings, v6.2.0

ERR2864242.results.txt

Thanks, Miguel Pinto

jodyphelan commented 5 months ago

Hi @insapathogenomics

Yes this should indeed be assnotated as conferring PZA resistance. The problem is that snpEff annotates this as an inframe deletion rather than a frameshift. The strict definitions given by the WHO catalogue only consider frameshifts for LoF and do not use the size of the deletion. I will add inframe deletions in pncA to the more "relaxed" version of the database (which is the default db for tb-profiler).