gatk4-basic-variant-validation

Simple workflow to validate a VCF (or GVCF) -- NOT Best Practices, only for teaching/demo purposes.

Inputs and outputs

Required inputs

• One VCF file or GVCF file and its index (can be bgzip/tabix)
• A list of intervals to process (for parallelization)
• Genomic resources: reference genome in FASTA format (.fasta) and its accessory files (.fasta.fai and .dict)

Optional inputs

• Resourcing and environment parameters including memory, disk space and container are all customizable

Outputs

• A list of text files (for each scatter chunk)containing the tool's standard output, which will contain the relevant error message if the tool encounters a validation error.

Important note: The tool will produce a non-zero return code if it finds an error. The Cromwell workflow management system considers this to mean the workflow failed even if the tool worked properly. In Terra, this will cause the workflow to be displayed as having failed, and the standard output file will not be added to the data model.