Regarding "bedaquiline" and "clofazimine" resistance

[mariaelf97]

Hello team,

Thank you for your great software!

While running some drug resistance prediction analysis I noticed that "bedaquiline" "clofazimine" are not listed in the results csv file. Is there a reason for that and do I need to use a specific flag for those?

Here is my rule for your kind reference!

rule run_mykrobe:
    input:
        r1=output_base + "reads/{isolate}_R1_001.fastq.gz",
        r2=output_base + "reads/{isolate}_R2_001.fastq.gz"
    output:
        output_base + "{run}/{isolate}/mykrobe.csv"
    conda:
        "mykrobe"
    shell:
        """
        mykrobe predict -S tb -s sample -i {input.r1} {input.r2} -o {output}
        """

[iqbal-lab]

sorry for the slow reply. The default panel for Mykrobe does not include bedaquiline or clofazimine resistance determinants. Right now we have not incorporated the WHOv2 panel, which had a lot of errors in it at the time of release. We'll have another look into whether we can add this.

[mariaelf97]

Thank you for your response. Do you happen to have a curated list of the variants and the reason for why you think they are error?

[iqbal-lab]

The WHOv2 panel originally came out in two documents, one VCF and another text (I forget precisely) which contradicted each other in various places. This meant that various bioinformaticians around the world spent a few months trying to fix it, and figure out what the correct panel was. Since the WHO doesn't really use version control, it was also tricky to keep track of, as they periodically updated the PDF online without updating version numbers or anything. I basically decided to wait until it was all cleared up. I've just contacted collaborators who were involved in the clean-up process, will see if we can incorporate now.

[mariaelf97]

Thank you very much- would be great to have a finalized version. Looking forward to hearing from you!

[mariaelf97]

@iqbal-lab Do you think this might be the latest version?
https://github.com/GTB-tbsequencing/mutation-catalogue-2023/commits/main/Final%20Result%20Files/WHO-UCN-TB-2023.7-eng.xlsx

I think they did not have it on github before. Looks like the last update was done in 2024 May.