Dev (#52)

* Updated to gatk4.1, Update VariantRecal syntax

* added samtools path variable

* Updated wording

* add a version of joint-discovery that takes in an array for gvcfs

* Update README.md

* increased mem for SNPsVariantRecalibrator for papiv2

* increased mem for SNPsVariantRecalibrator for papiv2

* increased memory to run on papiv2

* correction to variable names in json

* corrected parameter syntax for SNPsVariantRecalibrator task

* Updated haplotypecaller to WDL 1.0, removed comments from haplotypecaller #

* Added WDL 1.0 version of JointGenotyping to soon replace joint discovery wdl

* Update genotype2develop (#44)

* added updated joint-discovery wdl, needs testing

* Added place holder for terra verion of JointGenotyping wdl

* Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow

* updated the terra version of the JointGenotyping

* added urls for imports for JointGenotyping workflows

* Updated ReadMe

* Update genotype2develop (#45)

* added updated joint-discovery wdl, needs testing

* Added place holder for terra verion of JointGenotyping wdl

* Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow

* updated the terra version of the JointGenotyping

* added urls for imports for JointGenotyping workflows

* Updated ReadMe

* added missing runtime variables

* added missing runtime variable

* Update genotype2develop (#46)

* added updated joint-discovery wdl, needs testing

* Added place holder for terra verion of JointGenotyping wdl

* Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow

* updated the terra version of the JointGenotyping

* added urls for imports for JointGenotyping workflows

* Updated ReadMe

* added missing runtime variables

* added missing runtime variable

* Update genotype2develop (#48)

* added updated joint-discovery wdl, needs testing

* Added place holder for terra verion of JointGenotyping wdl

* Replaced joint-discovery with JointGenotyping workflow, added place holders for terra version for JointGenotyping workflow

* updated the terra version of the JointGenotyping

* added urls for imports for JointGenotyping workflows

* Updated ReadMe

* added missing runtime variables

* added missing runtime variable

* added recent updates from dsde-pipelines repo to terra version

* removed unnecessary optional override variables

* replaced '$' with '~'

* updated broad reference bucket path

* Add important notes regarding JointGenotype workflow to Readme

* minor update to Readme, renamed input file name in json

* minor spelling

* Added allele-specific annotations to HC command

* Updated import url to the next release tag

* correction to location of JointGenotyping input path location

* Added note regarding Reblocking GVCFS for GnarlyGenotyper

README.md

@@ -92,8 +92,9 @@ it easier to configure the workflow.*
 - JointGenotyping output is divided into lots of shards
   - desirable for use in [Hail](https://hail.is/), which supports parallel import
   - Its possible to use [GatherVcfs](https://gatk.broadinstitute.org/hc/en-us/search?utf8=%E2%9C%93&query=GatherVcfs) to combine shards.
+- Users working with large sample sets can invoke the GnarlyGenotyper task in the JointGenotyping.wdl workflow. However, the [ReblockGVCF](https://gatk.broadinstitute.org/hc/en-us/articles/360037593171-ReblockGVCF-BETA-) tool must be run for all GVCFs produced by HaplotypeCaller before they can be appropriately processed by GnarlyGenotyper. A workflow that applies the reblocking tool is provided here: [ReblockGVCF-gatk4_exomes_goodCompression](https://portal.firecloud.org/?return=terra#methods/methodsDev/ReblockGVCF-gatk4_exomes_goodCompression/4)
 - GnarlyGenotyper uses a QUAL score approximation
-  - dramatically improves performance compared with GenotypeGVCFs, but QUAL output (and thus 
+  - dramatically improves performance compared with GenotypeGVCFs, but QUAL output (and thus
     the QD annotation) may be slightly discordant between the two tools
 - The provided JSON is meant to be a ready to use example JSON template of the workflow. It is the user’s responsibility to correctly set the reference and resource input variables using the [GATK Tool and Tutorial Documentations](https://software.broadinstitute.org/gatk/documentation/).
 - Relevant reference and resources bundles can be accessed in [Resource Bundle](https://software.broadinstitute.org/gatk/download/bundle).