v0.17

What's Changed

• Add pipelines for benchmarking and cleaning SV VCFs by @rickymagner in #159
• Update IntervalList2Bed to handle case of compressed interval file inputs by @rickymagner in #163
• Update CleanSVs and some typos in BenchmarkSVs by @rickymagner in #162
• Implement FindSamplesAndBenchmark wrapper for SimpleBenchmark by @rickymagner in #164
• Update dashboards to use quickboard v0.4.0 by @rickymagner in #165
• Add Checkpointing and QC Collection to GlimpseImputation by @michaelgatzen in #161

Full Changelog: v0.16...v0.17

v0.16

What's Changed

• Added a pipeline for phasing VCFs and benchmarking their performance with WhatsHap (#124)
• New Utilities WDL: DownsampleAndCollectCoverage (#132)
• Update .dockstore.yml to include Dipcall (#135)
• Update for PRS on hg38 (#137)
• New workflow: CompareBenchmarks and fixed repo CircleCI (#103)
• Add combine summaries wf (#112)
• Add error messages in R scripts rather than just quit for PRSWrapper (#141)
• Update RTG docker for vcfeval to fix FORMAT filters ignored (#142)
• vcfdist evaluation (#143)
• Toggle benchmark vc fs fingerprint (#144)
• Potential improvements regarding default thread numbers and disk sizes (#150)
• Handle ploidy in chrX and chrY outside of the PAR region for benchmarking (#133)
• Add utility for creating IGV session from list of bams, vcfs, intervals (#145)
• Add utility for converting interval_list to bed efficiently (#154)
• Rewrite SimpleBenchmark and merge for staging before replacing BenchmarkVCFs (#155)
• Add MatchFingerprints utility WDL (#156)
• Automatic Novelty Detection/Flagging from PCA plots (#157)
• Add CMRG interval files to our docs (#158)
• Add Glimpse2Imputation pipeline (#123)
• Pandas deprecated DataFrame.append in PRS QC (#160)

Full Changelog: v0.15...v0.16

v0.15

• Multiqc in Terra (#125)
• Added WDLs for the RNA QC metric collection/concordance as part of a (#127)
• Long Read RNA Benchmarking Pipeline First Draft (#126)
• BCFTools docker: Added the python-is-python3 package (#129)
• Added Dipcall WDL and reformat README for utilities (#130)
• PRS check z-score before APOL1 correction (#131)

Full Changelog: v0.14...v0.15

v0.14

BenchmarkVCFs

• SimpleBenchmark -- a new WDL for benchmarking VCFs (#115)

Utilities

• Added documentation on Interval Files commonly (#118)
• Added missing comma in interval list input for Terra (#119)
• Added utilities for bam stats over intervals (#120)
• Added pysam docker, for use elsewhere by (#121)

PRS

• AggregatePRSResults updates by (#122)

Full Changelog: v0.13...v0.14

v0.13

PRS

• Lowercase pcs in results csv (#117)

Full Changelog: v0.12...v0.13

v0.12

PRS

• Partial Aggregation Set handling, refactor, and testing(#114)
• Aggregate PCs, add tests (#116)

Full Changelog: v0.11...v0.12

v0.11

Utilities

• Updated CollectBenchmarkSucceeded utility (#109)

Functional Equivalence

• FE: rewrote F1 evaluation using Pandas by (#97)
• Updated python-data-slim and using it in FunctionalEquivalence WDLs (#111)

PRS

• QC Report updates by (#113)

Full Changelog: v0.10...v0.11

v0.10

Imputation/PRS

• Handle situation where control sample is not resulted for one conditions (#106)
• Improved formatting of samples table in prs aggregation report (#107)
• Automatically deliver QC'd results file to delivery bucket (#108)

v0.9

Imputation/PRS

• Handle no-calls at APOl1 risk alleles in ckd adjustment (#62)
• Added HTML report feature (#69)
• PRS Reportable Range Check (#88)
• Aggregate PRS Output (#92)
• Add Interaction terms to PRS pipeline (#90)
• Notebook for manual QC editing of prs results table (#93)
• PRS: Interactive PCA plot (#94)
• Changed batch_id to lab_batch and is_control to is_control_sample (#95)
• Add --allow-extra-chr to GenotypeG1G2RiskAlleles by (#96)
• Separate training on population from application of ancestry adjustment in prs pipeline (#91)
• Pass through lab_batch in PRSWrapper, and dynamically find tables (#98)
• PRS missing sites QC (#99)
• Remove personal dockers in PRS pipeline (#100)
• Pass through is_control_sample (#101)
• Aggregate PRS: Added logic to compare control sample vs expected control results by (#102)
• Formatting improvements to aggregation report (#105)

FindSamplesAndBenchmark

• Fixing some issues and updating FindSamplesAndBenchmark (#86)

BenchmarkVCFs

• BenchmarkVCFs: Fixed a bug where NA is written to output files (#89)

General

• Fix copyright in license (#104)

v0.8

Imputation/PRS

• Added haplotype database input for validating imputation pipeline (#34)
• Made score adjustment optional (#37)
• Extra options for imputation pipeline (memory alloc for MergeSingleSampleVcfs- #36)
• Added some standard dockers (#29)
• Score vcf memory input change (#53)
• Use Plink for PRS scoring IDs (#58)
• APOL1 ckd adjustment (#59)
• Ancestry-dependent variance PRS score adjustment (#54)
• Added PRS wrapper script (#55), with percentile output (#83), and risk output as HIGH/NOT_HIGH (#85)
• Updated Cromwell from 47 to 66 (#63)
• Check FlashPCA (#60)
• Use loglink population correction for PRS (#72)
• Bug fixes and syntax error fixes (#38, #39, #42, #43, #45)

BenchmarkVCFs

• Using write_lines and dplyr to avoid bash char limit (#6)
• Made Shiny app public (#23)
• Added FindSamplesAndBenchmark (#41)
• Added some utilities and benchmarking changes (#44)
• Labels for eval vcfs in FindSamplesAndBenchmark and dummy input for Terra caching (#68)
• Use input vcf size to determine disk size in BenchmarkVCF (#71)
• Speed up ExtractSample step (#76)
• Modified default inputs and made more accessible to customize in Terra for FindSamplesAndBenchmark (#73, #74, #78, #79)
• Added utility for collecting subset of successful benchmarks when some failed on Terra (#81)
• Added some standard dockers as utilities (#84)

Functional Equivalence

• Added FE workflow (#27)

Build Haplotype Map

• Added BuildHaplotypeMap (#47)