# Copy/Paste from https://www.cog-genomics.org/plink/2.0/
28 Nov 2019: Fixed a VCF half-call handling bug introduced last month.
This is a candidate for the final alpha 2 build (which will remain available for download for several months).
16 Jan 2020: --pca allele/variant weight multithreading bugfix.
14 Jan: --make-king-table rel-check bugfix.
3 Jan 2020: Fixed --extract-if-info/--exclude-if-info numeric-argument bug introduced in late October.
30 Dec 2019 (alpha 3): This makes the following potentially compatibility-breaking changes:
--write-snplist and --indep-pairwise require all variant IDs to be unique. For --write-snplist, this can be overridden by adding the 'allow-dups' modifier.
.bgen/.gen import commands require the REF/ALT mode to be explicitly declared.
--glm defaults to 'firth-fallback' mode for binary phenotypes. The old behavior can be requested with the 'no-firth' modifier.
--glm errors out, instead of just skipping the phenotype and printing a warning, when there's a linear dependency between the phenotype and the covariates. The old behavior can be requested with the 'skip' modifier.
--pca's 'var-wts' subcommand has been replaced with 'allele-wts', which handles multiallelic variants properly. For datasets that contain only biallelic variants, the old output format can still be requested with 'biallelic-var-wts'.
PLINK 2 now errors out when you request an LD computation on a dataset with less than 50 founders. This can be overridden with --bad-ld.
--score's old NMISS_ALLELE_CT column (nonmissing allele count) has been renamed to ALLELE_CT, and the column set renamed accordingly, since in other contexts, 'nmiss' refers to the number of missing values, which is essentially the opposite...
--make-king-table's ID{1,2} columns have been renamed to IID{1,2}, for consistency with other PLINK 2 commands.
In addition, the GRM computation (along with "--pca approx" and "--score variance-standardize") now handles multiallelic variants properly, instead of just collapsing all minor alleles together; --score allows each allele in a multiallelic variant to be assigned its own score; and --glm handles categorical covariates in a manner that's less likely to cause VIF overflow.
29 Dec: Fixed a bug which affected processing of some heterozygous-double-ALT multiallelic variants, and a bug that caused ALT2/ALT3/etc. allele frequencies to not be properly initialized in some circumstances.
13 Dec: Fixed bug introduced in 22 Nov build which caused some reported dosages/counts (such as --freq's OBS_CT column) to be doubled. --loop-cats bugfixes.
28 Nov: Fixed a VCF half-call handling bug introduced last month.
26 Nov: Fixed recent bug which caused a segfault when no-duplicate-allowed variant ID lookup was performed with more than 16 threads.
