Drug Resistance Marker Detection
Generate a report summarizing drug resistance markers detected in a given set of variant calls.
Generate a report summarizing drug resistance markers detected in a given set of variant calls.
Workflow for analyzing drug resistance markers using variant data called by Oxford Nanopore long-reads. The workflow annotates variant calls, then searches for known drug resistance markers and summarizes this information in a report.
This workflow is maintained by the Broad Institute and is written in Workflow Description Language (WDL). Further documentation can be found here.
Drug Resistance Marker Detection workflow diagram
Workflow Inputs
The workflow takes an input VCF file and information about the path where the output report should be saved.
| Input | Description |
|---|---|
vcf |
VCF file to analyze for drug resistance markers |
dir_prefix |
Prefix for output directory |
gcs_out_root_dir |
GCS output root directory |
Workflow Outputs
The workflow outputs a drug resistance report in txt format in the specified GCS output bucket and path.
| Output | Description |
|---|---|
drug_res_report |
Summary report of drug resistance markers identified in the VCF file |
Containers
Containers used by the pipeline are hosted in the Broad Institute’s public container registry, and the public biocontainers registry in quay.io.