JointGenotypingWf.md

Workflow overview

This WDL pipeline implements joint calling across multiple samples according to the GATK Best Practices (June 2016) for germline SNP and Indel discovery in human whole-genome sequencing (WGS) data.

Data requirements/expectations :

• One or more human whole-genome per-sample GVCF files

List of Generated Outputs:

VCF Output Files

• output vcf
• output vcf index

VCF Metrics

• detail_metrics file
• summary metrics file

Output the interval list generated/used by this run workflow

• output intervals

Version notes

This is a pre-release version of the pipeline which does not include a fully runnable example dataset.