This adds a "patch" fix for #24 (until the underlying pandora problem can be resolved).
What we do is, for a variant with a "failed" (null) call, we check whether the variant spans the start codon. If it does, and the gene it is in is one where gene absence causes resistance, we call 'R' with a "start lost" tag.
After running the pipeline with this change, we get the following diff
Tool
Drug
ΔFN
ΔFP
drprg
Amikacin
0
0
drprg
Capreomycin
0
0
drprg
Delamanid
0
0
drprg
Ethambutol
0
0
drprg
Ethionamide
-24
5
drprg
Isoniazid
0
0
drprg
Kanamycin
0
0
drprg
Levofloxacin
0
0
drprg
Linezolid
0
0
drprg
Moxifloxacin
0
0
drprg
Ofloxacin
0
0
drprg
Pyrazinamide
-9
1
drprg
Rifampicin
0
0
drprg
Streptomycin
0
0
The FPs are also called start lost by tb-profiler so I guess the phenotypes could be wrong? Anyway, this is a good result.
This adds a "patch" fix for #24 (until the underlying pandora problem can be resolved).
What we do is, for a variant with a "failed" (null) call, we check whether the variant spans the start codon. If it does, and the gene it is in is one where gene absence causes resistance, we call 'R' with a "start lost" tag.
After running the pipeline with this change, we get the following diff
The FPs are also called start lost by tb-profiler so I guess the phenotypes could be wrong? Anyway, this is a good result.