The 21 Nov 2023 plink2 builds fix a serious issue with the double-precision logistic regression in Jan-Oct 2023 builds. (The issue did not affect older plink2 builds, the single-precision mode, or the Firth regression mode.) We recommend rerunning affected logistic regressions.
Major enhancements since the Mar 2017 build include:
- Linear regression that is often hundreds or even thousands of times as fast as PLINK 1.9, with no loss of accuracy.
- VCF dosage import/export.
- Most commonly-used PLINK 1.9 commands, with the remaining major exception of non-concatenating merge. (plink2's take on --r2 isn't done yet, but it should be completed within the next week.) Many rough edges in the PLINK 1.x form of these commands have been addressed.
- Several additional sanity checks (which can be overridden).