2.3.1

• Updated Haplotypecaller default GATK docker to 4.2.0.0

2.3.0

• Removed JointGenotyping workflow from this repo and added the new location for the workflow in Readme.
• Updated Haplotypecaller default GATK docker to 4.1.9.0
• Add dockstore.yml file to automatically update push from git to Dockstore

2.2.0

• Added requester pays option for Haplotypecaller workflow
• Updated JointGenotyping to 1.3.0 version from dsde-pipelines repo:
  • Fix SplitIntervals task so that it works for abutting WGS intervals. Increase by chromosome scatter count appropriately for WGS as fallback.

2.1.1

Removed Terra version of JointGenotyping. View pr55 for details

2.1.0

• Fix for user error message when using VCF mode for HC: gatk forum ticket
• HC command was updated to replicate dsde-piplines command. A conditional was added to use "AS_StandardAnnotation" only if make_gvcf is set to true
• HC workflow updated to use gatk4.1.7.0
• Removed suggested disksize in ReadMe

2.0.0

Updated haplotypecaller to WDL 1.0, removed comments from haplotypecaller JSON
Added allele-specific annotations to HC
Replaced joint-discovery with JointGenotyping workflow,
Added Terra version for JointGenotyping workflow
Added urls for imports for JointGenotyping workflows
Updated ReadMe to reflect changes to JointGenotyping workflow

1.1.2

Fixed SNPsVariantRecalibrator syntax for resources parameter issues:49

1.1.1

• SNPVariantRecalibrator runs out of memory on Papiv2. Provided an optional memory override and a default to 2*size(sites_only_variant_filtered_vcf, "GB" ). if default is lower then 7 GB memory sets to 7 GB.

1.1.0

• Updated to GATK4.1
• Update VariantRecal syntax to work for GATK4.1
• Added samtools path variable in haplotypecaller wdl
• Add a version of joint-discovery that takes in an array for gvcfs to be used on Terra/FC
• Set the docker version and disk size in the joint-discovery wdl, but made override options

1.0.4

• Added HaplotypeCaller NIO.
• Added disk sizing within task.
• Update gatk image to 4.0.6.0.
• Minor correction to picard command in JD.