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@rickymagner rickymagner released this 15 Dec 15:40
· 115 commits to main since this release
v0.8
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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)
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