From 3a789055de139fee2a347d5bb48cf55bfb878c2b Mon Sep 17 00:00:00 2001 From: bshifaw Date: Mon, 24 Feb 2020 14:22:47 -0500 Subject: [PATCH] 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 | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 5357ad8..8750dc0 100644 --- a/README.md +++ b/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).