five-dollar-genome-analysis-pipeline

This WDL pipeline implements data pre-processing and initial variant calling (GVCF generation) according to the GATK Best Practices (June 2016) for germline SNP and Indel discovery in human whole-genome sequencing and exome sequencing data. The provided intervals in the json are intended for whole-genome sequencing, users are expected to use thier own exome intervals for exome sequencing.

Note: For those users interested in running this wdl on FireCloud (FC), the FC version has been provided as fc_germline_single_sample_workflow.wdl. Please visit the FC featured methods and workspaces for more GATK Best Practices pipelines.