GenotypingBGWGSWorkflow
This workflow performs variant genotyping for genome samples, producing a fully annotated VCF file. It optionally fetches the input CRAM from a GCP data location before running GATK HaplotypeCaller and GenotypeGVCFs.
Input Parameters
| Type | Name | Req’d | Description |
|---|---|---|---|
| String | sample_id | Yes | Full sample identifier |
| String | accession_id | Yes | Sample accession (PM#) |
| String | gcp_project_id | No | GCP project ID |
This is a companion discussion topic for the original entry at github.com/mgbpm/biofx-workflows/GenotypingBGWGSWorkflow