Among other things, this includes:
- Non-concatenating merge
- --glm 'multinomial' modifier which enables multinomial logistic/Firth regression for categorical phenotypes. Likelihood-ratio (default), Wald, and score tests are supported.
- --ld-score and bundled ldsc/mtag utilities
- Import/export of BIMBAM Mean Genotype Format
- Multiallelic generalizations of the GCTA / PLINK 1.9 --ibc inbreeding statistics
- Reworked --flip-scan, which can check for allele flips relative to another reference dataset (instead of just relative to another subset of the current dataset), and considers allele frequences before LD
- Covariate-supporting epistasis scans
- Reworked --neighbour, which is now a port of bigsnpr's outlier detection method
- --meta-analysis, now including the Han & Eskin (2011) rnadom-effects test
- Additional --pca/GRM sanity check: it now errors out instead of producing unstable results when very-low-MAF variants are present
- Several memory-efficiency/speed improvements
- Hardening against malformed inputs
- Most other previously-unimplemented PLINK 1.9 flags; contact us about any still-missing functionality which you think should be preserved.