Genotyping Workflow and AnnotSV Updates

GATK Genotyping Workflow Update

This release updates the GATK Genotyping portion of our germline variant workflow. Previously the workflow had been written only with WGS samples in mind. This release updates the workflow so it can handle WXS and Targeted Sequencing inputs. The key difference between WGS and WXS/Targeted calling is in the variant filtration process. WGS samples will be processed using VQSR; WXS/Targeted samples will be processed using HardFiltering. Users can now specify the experiment_type of the input and the workflow will perform the appropriate filtration.

Accompanying this update, we've also added a new output called gatk_annotation_plots. This TAR.GZ file contains a series of plots of the key genotying annotations used for the HardFiltering process. As it is associated with HardFiltering, this output will only be created if the sample is WXS/Targeted.

We've also updated the GATK dockers used for a number of the utility functions used in the genotyping workflow. These functions include gathering VCFs, tranches, etc and should have no impact on the final outputs.

Other Functional Updates

• Two new outputs to the germline workflow:
  • AnnotSV-annotated version of CNVnator's cnvnator_vcf output
  • AnnotSV-annotated version of GATK's gatk_gcnv_genotyped_segments_vcfs output
• Adjustments were made to the germline workflow to make some inputs no longer required; since pretty much everything can be turned off/on, requirements mostly depend on what you are trying to do
• Opened extra argument ports for various tools in the workflow. Gives the user more control of the run

Documentation Updates

This release also contains a series of documentation updates:

• Fixing the Broad GCP links in the docs
• Updated docs to include new outputs

What's Changed

• 📚 update gcp docs by @dmiller15 in #48
• 🎉 add annotsv to CNVnator and docs by @dmiller15 in #49
• 🔧 annotsv gatk gcnv out by @dmiller15 in #50
• 🔧 GenomicsDBImport extra args init by @dmiller15 in #52
• 🤖 add docker table builder ghas by @dmiller15 in #54
• 🚧 exome/panel genotyping by @dmiller15 in #53
• 🎉 add hardfilter annotation filter plotting by @dmiller15 in #59
• 🐳 update gatk dockers by @dmiller15 in #61
• 🔖 genotyping release prep by @dmiller15 in #64

Full Changelog: v1.1.1...v1.2.0