1.2.0

Updated Wdls to match dsde-pipelines repository. Changes included:

• Updated memory "G" to "Gib"
• Disk and memory adjustments
• Renamed BamToGVCF.wdl to VariantCalling.wdl
• Make WGS pipeline use GATK3 for GermlineSingleSample

1.1.0

• Updated to latest script from dsde-pipelines/pipelines/dna_seq/germline/wgs/WholeGenomeGermlineSingleSample.wdl
• Update Includes the use of WDL version 1.0
• Removed Firecloud wdl version as it is not compatible with the latest subworkflows
  Imports use git url

Bug fix:
#17

1.0.3

• Switched imports to git url tag releases

Note: This release uses an older version of the pipeline that uses wdl draft 3. Please use release 1.1.0 or later for most updated scripts.

1.0.2

• Removed wording indicating pipeline can be used for exomes.

Split ReadGroup task bug fix

• Fix for splitRG task.
• Disk sizing now takes place within tasks.

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.