1.2.0

The preprocessing workflow is no longer Broad's production workflow, please visit five-dollar-genome-analysis-pipeline for the workflow currently being used in production.

• increased disk space for BaseRecal and ApplyRecal
• replaced sub_sub with basename() issue 14

1.1.2

• Updated script to match dsde-pipelines
• Replaced gatk4 version of single sample with fc version
• Added important note to readme, included note related to Joint Genotype

1.1.1

• Switch the docker image for the JointGenotyping from temporary image to the official version.

Bug fix and Docker Change.

• Update JointGenotyping to fix GatherTranches bug.
• Added a temporary docker image to be used to execute JointGenotyping. Built using build_gatk4_joint_genotyping_docker.sh .
• distinguish gatk4 version requirements for PairedEndSingleSampleWf and JointGenotypingWf in the ReadMe

Initial release of the pre-processing + GVCF generation workflow

This release comprises the workflow that goes from unmapped BAM (uBAM) to GVCF for a single WGS sample, including all QC steps. That workflow is optimized for cost on the Google Cloud Platform. In its current form it will NOT run on other platforms due to the use of Google's NIO streaming protocol. A platform-agnostic version will be made available in a separate repository in the near future.