AutoGVP - release v1.0.1

What's Changed

• Add DOI for final submission to README by @jharenza in #232
• copy autogvp scripts to Dockerfile by @rjcorb in #233
• Rjcorb/234 update variant ids col by @rjcorb in #236
• retain gnomad non-cancer AF popmax in final autogvp output by @rjcorb in #237
• rm leading semicolon in variant_ids by @rjcorb in #240

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

AutoGVP - release v1.0.0

What's Changed

• update docker image to v1.0.0 by @jharenza in #230

Full Changelog: v0.4.3...v1.0.0

Release v0.4.3

What's Changed

• Fix broken link for column names by @jharenza in #210
• Update cavatica workflow to allow for input of external clinvar vcf by @rjcorb in #212
• updated readme addressing reviewer comments by @naqvia in #213
• fix submission file loading bug by @rjcorb in #218
• Add ClinVar origin columns to AutoGVP output by @rjcorb in #219
• Update germline-pathogenecity_flow.png by @jharenza in #221
• update select-clinvar-submissions.R to only consider P,LP,B,LB,VUS submissions by @rjcorb in #223
• update README by @rjcorb in #225
• add lubridate to Dockerfile by @rjcorb in #227

Full Changelog: v0.4.2...v0.4.3

Release v0.4.2

What's Changed

• readme-update-with-wiki by @jharenza in #204
• Update docker commands to numeric by @jharenza in #205
• add all clinvar disease concept ID file by @rjcorb in #207
• add cancer predisposition gene list by @rjcorb in #209

Full Changelog: v0.4.1...v0.4.2

Release v0.4.1

What's Changed

• add clinvar cols to abridged output by @rjcorb in #200
• rm address_conflicting_interpretations() function and command by @rjcorb in #202
• Update README.md - figure commit by @jharenza in #198

Full Changelog: v.0.4.0...v0.4.1

Release v0.4.0

What's Changed

• Include variant depth in final output by @rjcorb in #176
• Rjcorb/173 add descriptive clinvar revstat by @rjcorb in #174
• Take original intervar call when PVS1=0 by @rjcorb in #178
• Update README.md by @jharenza in #181
• Add AD columns to output by @rjcorb in #180
• add curl to Dockerfile by @rjcorb in #187
• Update repo directory structure by @rjcorb in #184
• Update wrapper script conditionals and base directory by @rjcorb in #185
• Save final ClinVar and InterVar calls for all variants by @rjcorb in #189
• Flag conflicting clinvar variants with >= 1 P/LP submission in final output by @rjcorb in #193
• add disease list, strategy options to select-clinVar-submissions.R by @rjcorb in #192
• Rjcorb/194 fix select submission bug by @rjcorb in #195
• Update germline-pathogenecity_flow.png by @jharenza in #196
• Update README.md by @jharenza in #197

Full Changelog: v.0.3.0...v.0.4.0

AutoGVP - first beta release!

What's Changed

• Add pathogenicity assessment workflow by @naqvia in #7
• Adding --vcfinput flag to pathogenicity by @sakshamphul in #8
• Update 02-annotate_variants_user.R by @jungkim2 in #9
• Review non cavatica by @naqvia in #13
• cleaned files and directories by @naqvia in #16
• revamp the README by @jharenza in #20
• Bp6 removal by @naqvia in #22
• add some missing steps to readme by @jharenza in #26
• Update dockerfile by @naqvia in #33
• 🧹 rm dirs from cwl dev by @migbro in #30
• add links to each tool and specify autoPVS1 version by @jharenza in #35
• Requesting to change files for testing input by @jungkim2 in #37
• Update .gitignore by @jharenza in #38
• Feature/refactor by @sakshamphul in #25
• cavatica test files by @naqvia in #41
• cavatica workflow test run by @naqvia in #34
• Refactor cavatica R script by @sakshamphul in #53
• smaller testing input, modified readme to reflect file name by @jungkim2 in #48
• intervar adjustment issue by @naqvia in #49
• Add columns to abridged output by @rjcorb in #57
• Fix intervar issue by @naqvia in #61
• update multianno and intervar df sorting by @rjcorb in #59
• Filtering script by @naqvia in #58
• modified dockerfile to install bcftools by @naqvia in #56
• Modify address_ambiguous_calls() function by @rjcorb in #67
• Remove gnomad, variant AF and depth filtering by @rjcorb in #68
• further removed filtering info from comments, options, and functions by @naqvia in #69
• filter multianno,intervar,autopvs1 files for vcf variants by @rjcorb in #71
• add issue and PR templates by @rjcorb in #70
• Parse VCF file so that INFO subfields are tab-separated columns by @rjcorb in #74
• test styler action by @jharenza in #75
• Issue77 by @naqvia in #78
• removed variants from intervar run that got a call from submission files by @naqvia in #72
• de-duplicate info field columns in parsing script by @rjcorb in #79
• fixed filtering by checking vcf_id df by @naqvia in #84
• update download script to pull from S3 by @jharenza in #86
• checks if required user input files exist and if variants match by @naqvia in #44
• Update filter vcf script with pass filter by @rjcorb in #90
• retain all INFO fields when parsing by @rjcorb in #93
• deleted unnecc results dir by @naqvia in #92
• resolve discordant calls between variant_summary and submission_summary by @rjcorb in #96
• issue85 bug by @naqvia in #94
• Create comprehensive AutoGVP output by @rjcorb in #98
• Add script to select clinVar variant submissions by @rjcorb in #105
• Add gene annotation filtering, final output script by @rjcorb in #99
• Update 01-annotate_variants_custom_input.R by @jungkim2 in #108
• Update 01-annotate_variants_custom_input.R by @jungkim2 in #109
• deleted file by @naqvia in #112
• Issue116 by @naqvia in #117
• modified code to address issue111 by @naqvia in #113
• Update 01-annotate_variants_custom_input.R by @jungkim2 in #110
• wrapper script by @naqvia in #97
• Update 01-annotate_variants_custom_input.R by @jungkim2 in #118
• Add new test file that captures different scenarios by @jungkim2 in #121
• Modify address_ambiguous_calls() function to exclude likely pathogenic clinvar calls by @rjcorb in #124
• Set clinvar clinsig equal to clinvar final call by @rjcorb in #126
• Fix filter vcf script so first filtering criterion is applied by @rjcorb in #128
• update clinvar star assignment code by @rjcorb in #134
• update address_conflicting_interp() by @rjcorb in #135
• modify loading of annotation files by @rjcorb in #136
• modify clinvar star assignment for no interpretation variants by @rjcorb in #139
• create var id cols to match multianno & intervar variants by @rjcorb in #141
• Filter multianno, autopvs1, intervar files before loading in R by @rjcorb in #143
• readme update by @naqvia in #123
• Select AutoPVS1 transcript as final variant annotation by @rjcorb in #145
• rm duplicate cols in intervar/multianno dfs by @rjcorb in #147
• Set resolved ClinVar calls to Stars == "1" by @rjcorb in #149
• add guess_max when loading files by @rjcorb in #151
• Fix filtering in custom autogvp workflow to retain all variants by @rjcorb in #153
• Save criterion and adjusted evidence cols in final output by @rjcorb in #155
• Add output directory argument by @rjcorb in #157
• rename scripts by @rjcorb in #159
• update awk statement for INFO field extraction by @rjcorb in #161
• add sample id column to final output by @rjcorb in #163
• replace %3D with = in HGVSp by @rjcorb in #165
• remove submissions with no assertion criteria when selecting ClinVar calls by @rjcorb in #168
• remove associated pheno criterion from ClinVar submission selection by @rjcorb in #172
• merge P/LP and B/LB submissions when selecting consensus call by @rjcorb in #170

New Contributors

• @naqvia made their first contribution in #7
• @sakshamphul made their first contribution in #8
• @jungkim2 made their first contribution in #9
• @jharenza made their first contribution in #20
• @rjcorb made their first contribution in #57

Full Changelog: v0.2.0...v.0.3.0

Pathogenicty Preprocessing Workflow

Release highlights

• Ported over autoPVS1
• Edited wrapper and support scripts to run inside and outside of cwl environment
• Added direct-from vcf read supports - skips VEP as input is assumed to be already annotated
• Created workflow to run InterVar (with Annovar run step) and autoPVS1 to generate all necessary files to filter for pathogenic variants

What's Changed

• 🤖 Create pathogenicity preprocessing wf by @migbro in #3

Full Changelog: v0.1.0...v0.2.0

InterVar Workflow

This is a beta release to start creating a more comprehensive pathogenicity workflow. Starting with a workflow to take in a VCF file, and annotate with ANNOVAR and score with InterVar