Resistance¶

Depends on the Epidemiology workflow (for genotyping samples)

Parameters¶

species: Species name to determine which software are available to run for your sample

Available softwares¶

Mycobacterium tuberculosis specific analyses¶

If the value of species is Mycobacterium_tuberculosis, specific variant markers of resistance can be searched by mapping to the genome of H37Rv, genotyping with GATK and annotating the resulting VCF. Different sources of annotation can be used to search markers:

Deliverables¶

rgi and mykrobe analysis¶

report/resistance/rgi_summary.xlsx: summary of RGI results for every samples (one per sheet)
report/resistance/mykrobe_summary.xlsx: summary of Mykrobe results for every samples (one per sheet, only for Mycobacterium genus or Staphylococcus aureus)
report/resistance/{sample}_rgi_report.html: summary of RGI results as html document with cross references to the CARD database

Mycobacterium tuberculosis SNPs variant associated to resistance¶

sample/{sample_name}/resistance/bwa/miotto_high_moderate_minimum_confidence_annotated/mutations.vcf: VCF files of all markers in Miotto et al. 2017 European Respiratory Journal
sample/{sample_name}/resistance/bwa/mykrobe_annotated/mutations.vcf: VCF files of all markers in Bradley et al. 2015 Nature Communications
sample/{sample_name}/resistance/bwa/walker_resistant_annotated/mutations.vcf: VCF files of all markers in Walker et al. 2015 Lancet Infectious Diseases
sample/{sample_name}/resistance/bwa/rgi_annotated_full_2_0_0/mutations.vcf: VCF files of all markers in version 2.0.0 of the CARD database