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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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Missing Fluoroquinolone profile in the itol reports #331

Closed emilyncosta closed 6 months ago

emilyncosta commented 7 months ago

Dear Jody,

Working in analyzing the TB-Profiler outputs within the MAGMA pipeline using distinct datasets I realized that while the DR is classified as Pre-XDR based on the output "joint.major_variants.dr.itol.txt", the individual variants from output "joint.major_variants.dr.indiv.itol.txt" does not reflect the FLQ (LEVO or MOX) resistance.

CC @abhi18av @TimHHH @vrennie

Thanks for helping ;)

Emilyn.

jodyphelan commented 6 months ago

Hi @emilyncosta

Thankd for sharing, I'll take a look at that bug!

abhi18av commented 6 months ago

Hi @jodyphelan ,

Glad to see the latest v6.0.0 release https://github.com/jodyphelan/TBProfiler/releases/tag/v6.0.0 🎉

Any chance that this bug would be addressed in patch release soon?

jodyphelan commented 6 months ago

Hi @abhi18av ,

If I'm understanding correctly, the previous version showed Pre-XDR from the drug resistance itol colour strip, however no fluoroquinolone resistance was being shown on the individual drugs annotation. Is that correct?

The new version should correct this, e.g. see below:

1Uf5YaLzP82A2EaPRK8Jgg

abhi18av commented 6 months ago

however no fluoroquinolone resistance was being shown on the individual drugs annotation. Is that correct?

Yes, that is spot on! I can confirm that this has been resolved with the latest v6.0.0 release and you can mark this issue as closed now :)

Thank you for the prompt fix @jodyphelan !

jodyphelan commented 6 months ago

Great!