Add some common resistance-conferring mutations that do no exist in population graph about drprg HOT 8 CLOSED

The model behind Gt conf is only meaningful for majors, so I'd bin it for minors

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This seems to have worked reasonably well

Quite a few ETO FPs though, which I will take a look at before moving on

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So all of those "new" ETO FPs are strong calls for a mutation I recently added (fabG1 L203L) which mykrobe and tb-profiler also call.

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This sounds great!

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The delamanid FPs are caused by us calling minor alleles for ddn L49P. One of these is backed up by the other callers, one seems like a decent minor call, but not made by the other callers, and the rest are very low depth. This has made me realise I am not applying the same variant filters to the minor allele calls as I do the normal major allele calls. For instance, some of these delamanid minor calls only have depth 2x on the minor allele, so these should be filtered out

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So, stepping back, what are the rules we want to apply to call a minor? Above x% of the total reads at that variant (either allele) and above some min absolute number, right? I'd think no other filters?

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The extra EMB FPs are also the same reasons as the delamanid ones.

I think we can just use the same filters for minors as we do for majors.

• Min. depth 3x
• At least one read on each strand
• Min. GT CONF 5 (which doesn't really apply to minor alleles I guess so we could bin this or just leave it in as it seems unlikely?)

We also have an FRS for majors, which we obviously don't want for minors

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Adding in the filtering of minors gives this diff to the results above

So the diff for this overarching issue is

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