they are employing multiple threads. Nonstandard '0/.' and similar VCF GT field values are now processed as if they did not have the trailing. 24 May: Sample-major to variant-major.bed transposition bugfix. filter can now match against more than one value. You are not alone. As a general rule, you shouldn't expect to keep REF/ALT alleles straight with plink.x, but we tried to make A2 consistently reference in these files and still didn't quite succeed; sorry about that. 4 July: Fixed two merge bugs which potentially caused data in the last few samples of an input or merged fileset to be mishandled. indep-pairwise results should no longer be slightly discordant with plink.07 when missing data is present (standard deviations were previously calculated once per site, they're now recalculated for every pair). check-sex/-impute-sex now has a 'y-only' mode. On a related note, if you are aware of an implementation of a plink command which is substantially better what we currently do, let us know; we'll be happy to switch to their algorithm and give them credit in our documentation and papers.
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1 July: Fix recently introduced (sorry about that) -data/-gen/-sample command-line parsing bug. 17 November: -r/-r2 bugfix, -fast-epistasis, -recode oxford. But if you used the unaff rows in the -hardy report for anything, you should rerun -hardy with the latest build.) set-test multiple-testing correction now counts nonempty sets with zero significant variants. mac/-max-mac added to development build. See the credits page for a partial list of people to thank. 16 October: Basic lasso implementation (-lasso).
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