Comments (8)
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
Tool | Drug | ΔFN | ΔFP |
---|---|---|---|
drprg | Amikacin | 0 | 0 |
drprg | Capreomycin | 0 | -1 |
drprg | Delamanid | 0 | 5 |
drprg | Ethambutol | -1 | 4 |
drprg | Ethionamide | -52 | 22 |
drprg | Isoniazid | 0 | 0 |
drprg | Kanamycin | 0 | 0 |
drprg | Levofloxacin | 0 | 0 |
drprg | Linezolid | -1 | 0 |
drprg | Moxifloxacin | 0 | -1 |
drprg | Ofloxacin | 0 | 0 |
drprg | Pyrazinamide | -2 | -1 |
drprg | Rifampicin | -5 | 0 |
drprg | Streptomycin | 0 | 0 |
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
Tool | Drug | ΔFN | ΔFP |
---|---|---|---|
drprg | Amikacin | 0 | 0 |
drprg | Capreomycin | 0 | 0 |
drprg | Delamanid | 0 | -1 |
drprg | Ethambutol | 0 | -2 |
drprg | Ethionamide | 0 | 0 |
drprg | Isoniazid | 0 | 0 |
drprg | Kanamycin | 0 | 0 |
drprg | Levofloxacin | 0 | -1 |
drprg | Linezolid | 0 | 0 |
drprg | Moxifloxacin | 0 | -1 |
drprg | Ofloxacin | 0 | 0 |
drprg | Pyrazinamide | 0 | 0 |
drprg | Rifampicin | 0 | -1 |
drprg | Streptomycin | 1 | 0 |
So the diff for this overarching issue is
Tool | Drug | ΔFN | ΔFP |
---|---|---|---|
drprg | Amikacin | 0 | 0 |
drprg | Capreomycin | 0 | -1 |
drprg | Delamanid | 0 | 4 |
drprg | Ethambutol | -1 | 2 |
drprg | Ethionamide | -52 | 22 |
drprg | Isoniazid | 0 | 0 |
drprg | Kanamycin | 0 | 0 |
drprg | Levofloxacin | 0 | -1 |
drprg | Linezolid | -1 | 0 |
drprg | Moxifloxacin | 0 | -2 |
drprg | Ofloxacin | 0 | 0 |
drprg | Pyrazinamide | -2 | -1 |
drprg | Rifampicin | -5 | -1 |
drprg | Streptomycin | 1 | 0 |
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Related Issues (20)
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