VRSAnnotator

Description

GA4GH VRS identifiers provide a standardized way to represent genomic variations, making it easier to exchange, harmonize, and integrate genomic information.

This WDL workflow wraps the functionality of vrs-python's vcf_annotator, allowing you to annotate Variant Call Format (VCF) files with GA4GH Variation Representation Specification (VRS) Allele IDs on Terra! This makes integration of genomic variant data with downstream evidence data like MetaKB much easier.

To get started, navigate to the VRS AnVIL workspace to run it on Terra! For more details, see the docs on setting up a Terra workflow and the Dockstore repository for the VRS Annotator workflow.

Inputs

• input_vcf_path (File): Google resource path of VCF file (gs://)
• output_vcf_name (String): Name of annotated VCF file with its file extension (vcf.gz)
• seqrepo_tarball (File, optional): Google resource path for seqrepo tarball (tar.gz). Defaults to tarball stored in the requestor pays VRS AnVIL Workspace.
• compute_for_ref (boolean, optional): Whether to compute both the ref and alt allele or compute only the alt allele for each variant. Defaults to true, computing both.
• vrs_attributes (boolean, optional): Whether to compute both the ref and alt allele or compute only the alt allele for each variant. Defaults to true, computing both.
• genome_assembly (String, optional): genome assembly or genome build used by the VCF. Defaults to "GRCh38", but "GRCh37" is also supported.

Outputs

To write output file paths to directly to a Terra data table, specify the outputs, specifically:

• output_vcf (File): column in a Terra data table to write the output VCF to
• output_vcf_index (File): column in a Terra data table to write the tabix output VCF index to

For more info on how to write workflow ouputs to the data table, see the Terra docs