# 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)](https://openwdl.org/). Further documentation can be found [here](https://broadinstitute.github.io/long-read-pipelines/workflows/ONTPfTypeDrugResistanceMarkers/).

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](https://console.cloud.google.com/gcr/images/broad-dsp-lrma), and the public [biocontainers registry](https://quay.io/organization/biocontainers) in quay.io.