ExpandedDrugResistanceMarkerExtraction

ExpandedDrugResistanceMarkerExtraction

author

Jonn Smith

description

Extract drug resistance marker information from a single-sample VCF.

Inputs

Required

• dir_prefix (String, required): Directory prefix to use for finalized location.
• gcs_out_root_dir (String, required): GCS Bucket into which to finalize outputs.
• gene_drug_resistance_list (File, required): List of genes over which to include any variants in the expanded drug resistance report.
• protein_drug_resistance_list (File, required): List of specific protein changes to include in the expanded drug resistance report.
• sample_name (String, required): Name of the sample in the given single-sample VCF file.
• snpeff_db (File, required): SNPEff database file to use for functional annotations (if necessary).
• vcf (File, required): Input VCF.gz file containing variant calls from which to create an expanded drug resistance marker report.
• FunctionallyAnnotateVariants.snpeff_db_identifier (String, required)

Optional

• CallDrugResistanceMutations.runtime_attr_override (RuntimeAttr?)
• FinalizeAnnotatedVCF.keyfile (File?)
• FinalizeAnnotatedVCF.name (String?)
• FinalizeAnnotatedVCF.runtime_attr_override (RuntimeAttr?)
• FinalizeAnnotatedVCFIndex.keyfile (File?)
• FinalizeAnnotatedVCFIndex.name (String?)
• FinalizeAnnotatedVCFIndex.runtime_attr_override (RuntimeAttr?)
• FinalizeDRReportAllMarkers.keyfile (File?)
• FinalizeDRReportAllMarkers.name (String?)
• FinalizeDRReportAllMarkers.runtime_attr_override (RuntimeAttr?)
• FinalizeDRReportProteinMarkers.keyfile (File?)
• FinalizeDRReportProteinMarkers.name (String?)
• FinalizeDRReportProteinMarkers.runtime_attr_override (RuntimeAttr?)
• FinalizeSnpEffGenes.keyfile (File?)
• FinalizeSnpEffGenes.name (String?)
• FinalizeSnpEffGenes.runtime_attr_override (RuntimeAttr?)
• FinalizeSnpEffSummary.keyfile (File?)
• FinalizeSnpEffSummary.name (String?)
• FinalizeSnpEffSummary.runtime_attr_override (RuntimeAttr?)
• FunctionallyAnnotateVariants.runtime_attr_override (RuntimeAttr?)

Defaults

• do_functional_annotation (Boolean, default=true): If true, will perform functional annotation on the input VCF file prior to extracting drug resistance marker information.

Outputs

• drug_res_report_all (File)
• drug_res_report_prot_only (File)
• annotated_vcf (File?)
• annotated_vcf_index (File?)
• snpEff_summary (File?)
• snpEff_genes (File?)

Dot Diagram