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mbhall88 / head_to_head_pipeline

Snakemake pipelines to run the analysis for the Illumina vs. Nanopore comparison.
GNU General Public License v3.0
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Try mykrobe with a lower proportion of expected depth #81

Closed mbhall88 closed 2 years ago

mbhall88 commented 2 years ago

Based on the results in #80, we will try mykrobe with a lower expected proportion of expected depth as there were a number of Illumina missed resistance calls due to this filter - which is set to 30% by default.

mbhall88 commented 2 years ago

With an expected depth of 0.25 we get the following changes

Genotype concordance

1 less isoniazid FP and 1 less streptomycin FP.

Phenotype concordance

Nanopore results remain unchanged.
Illumina has 1 less streptomycin FN.

mbhall88 commented 2 years ago

With an expected depth of 0.20 we get the following changes

Genotype concordance

1 less amikacin (also capreomycin and kanamycin) FP. 1 less isoniazid FP.
3 less streptomycin FP.

Phenotype concordance

Nanopore results remain unchanged.
Illumina has 1 less amikacin FN
1 less streptomycin FN
1 more streptomycin FP

mbhall88 commented 2 years ago

Do you want to use any of these lower expected depths @iqbal-lab ?

mbhall88 commented 2 years ago

I'm going to close this as I think 0.2 has yielded very good results. Happy to change if you have strong feelings.