📝 SNV HotSpot Updates

We have identified the following important cancer HotSpots to be of interest in addition to our existing list:

H3C3, amino acid position 28
H3C14, amino acid position 28
H3C14, amino acid position 35

This update simply updates the default file pull for SNV HotSpot annotation for these rare but important cancer variants

What's Changed

• ✏️ update docs with bench critieria by @migbro in #20
• 🤖 Update Annotation Submodule for Release v1.2.3 by @migbro in #23
• 📝 update snv hotspot refs by @migbro in #22
• 📝 Bump wf version by @migbro in #24

Full Changelog: v1.0.0...v1.0.1

Kids First DNA Tumor Only Workflow v1.0.0

Release Notes

Filtration Updates

• Added README on Mutect2 Tumor Only Filtration recommendations: docs/MUTECT2_TUMOR_ONLY_FILTERING.md
• Updated README with new recommended gatk_filter_name and gatk_filter_expression values
• Added new default to filtermutectcalls_extra_args to filter calls with AF < 0.01

Annotation Updates

• Annotation workflow upgraded to version 1.2.1

Workflow Optimization

• ControlFREEC pileup creation now handled by a GNU parallel samtools implementation; no longer performing pileup on ALT contigs
• Interval creation and handling now matches what we have in the somatic workflow; user provides calling_regions, blacklist_regions, and cnv_blacklist_regions which are then processed by prepare_regions.cwl
• Added interval manipulation tools: awk_chrlen_builder.cwl, gatk_bedtointervallist.cwl, gatk_intervallisttobed.cwl, and gatk_intervallisttools.cwl
• Added switches to enable/disable all subworkflows of the tumor only workflow
• Move AnnotSV inside Manta subworkflow
• samtools calmd now only runs when the input is CRAM or if user specifies run_calmd_bam
• Styling cleanup for some tools and workflows

Quality of Life

• Added default of [2,3,4] to cfree_ploidy
• Reference input simplified to a single input with secondaryFile indexes rather than separate inputs for FASTA, FAI, and DICT
• Added suggestedFiles for indexed_reference_fasta, gem_mappability_file, panel_of_normals, blacklist_regions, and cnv_blacklist_regions

What's Changed

• ✨ Upgrade Annotation for Tumor Only by @dmiller15 in #10
• 🤖 Update Annotation Submodule for Release v1.2.0 by @migbro in #12
• 📚 add filter docs by @dmiller15 in #14
• 🚧 update tumor only workflow by @dmiller15 in #16
• 🧹 v1.0 release prep by @dmiller15 in #19

Full Changelog: v0.4.1-beta...v1.0.0

Hotfix for FilterMutectCalls

What's Changed

• 🐳 bump filtermutectcalls docker by @dmiller15 in #9

Full Changelog: v0.4.0-beta...v0.4.1-beta

🛠️ Annotate Prepass in Mutect2

This change has several documentation fixes and updates as well as eliminates the mutect2 filtered file in favor of having the protected output be an annotated version of that

• Allows for hotspot to be annotated on the mutect2 file containing soft filters to capture potential important hits
• Tumor only filtering is sort of an art - allows user to change filter params as needed if D3b defaults are not satisfactory

What's Changed

• Feature/mb update annot by @migbro in #8

Full Changelog: v0.3.0-beta...v0.4.0-beta

🔌 Add sample name override + annotSV

Functionality ported from somatic wf, it's not always possible to have the cram SM: match desired output vcf sample name, so added "old_tumor_name" input for GATK compatibility. Also added annotSV step for convenient SV annotation.

What's Changed

• 🔌 Add mismatch sample name + annotSV by @migbro in #7

Full Changelog: v0.2.0-beta...v0.3.0-beta

💪 DNA Annotation Upgrade

We've upgraded our annotation workflow to incorporate a more relatively recent gene model annotation as well as new annotation sources

Annotation changes

• Upgrade from VEP cache 93 to VEP cache 105 merged. This merged cahce also contains refseq annotations
• HGVSg field now also added
• Upgrade from using gnomAD v3.0.0 to v3.1.1. gnomAD has since expanded their sample size and also adjusted their VQSR scoring, improving our population frequency screening for public file outputs
  This uses as a git submodule the annotation workflow from the KF soamtic wf, v4.3.0

What's Changed

• 🔨 Upgrade DNA Annotation by @migbro in #6

Full Changelog: v0.1.1-beta...v0.2.0-beta

Bug Fix

An adjustment to the samtools calmd tool broke the tool itself, so I fixed the tool while maintaining the performance

KFDRC Tumor-Only Workflow Beta Release

This sets the groundwork for a more complete, prod-ready tumor-only workflow. Included in this release are:

• Xenome tools to preprocess PDX samples, if applicable
• A workflow wrapper to run Mutect2 from GATK 4.2.2.0 (SNV), ControlFreeC v11.6 (CNV) and Manta v1.4.0