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v2.0.0-beta.2
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@nebfield nebfield released this 31 Jul 11:59
· 8 commits to main since this release
v2.0.0-beta.2
69c467e
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Learn about vigilant mode.

Changelog

Features

  • Add FID support internally (FID + IID must be unique for all samples) [@nebfield, thanks to @jasamack for initial draft fix]
  • Add parameters to tune target variant missingness (--pca_geno_miss_target, default maximum 10%) and/or MAF (--pca_maf_target, default no filtering) during intersection with the reference panel. [@smlmbrt]
    • The new defaults will help incorrect ancestry assignments when running the calculator on low sample sizes (revert to pre-beta version behaviour), as this behaviour was caused by the MAF filter before.
  • Add --efo_id parameter, deprecating --trait_efo which will be removed in a future release

Misc

  • Remove default anaconda channels because of license changes #342

Contributors

smlmbrt, nebfield, and jasamack
Assets 2
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