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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. The final alpha 2 build has been tagged in GitHub, and will remain downloadable from here for the next several months.

The online documentation is now almost complete. The sidebar search box works. Stricter blank-line policy for most text input files: they're allowed at the end since this happens every once in a while with manually edited files , but they're no longer allowed elsewhere. Strings which start with a number but contain nonnumeric content e. Alpha 3 will introduce an 'allele-wts' modifier which generates one weight per allele instead; this is necessary to support multiallelic variants in an analytically sound manner.

This is designed to reverse --set-all-var-ids. Windows BGZF compression is now multithreaded. Improved read-error messages. Source code now supports dynamic linking with libzstd though performance may suffer if you don't build the multithreaded version of that library. Automatic Zstd text-file decompression was broken for a few commands by the 28 Sep build; that should work properly now. SID-loading bugfix.

Automatic-rename when an input filename matches an output filename should work properly again instead of erroring out though it should still be avoided. This bug only affected runs where --tests was invoked with 4 or more predictors. Fixed rare --glm bug that could cause all results to be reported as 'NA' when exactly one covariate is defined. Loaded allele frequencies are not recomputed any more. This only affected the last few samples of the file, but if you used --haps with an earlier build, we strongly recommend rerunning it.

A draft PGEN specification is now available. Brackets in command-line help text are now used in a manner more similar to other tools. Fixed a bug which occurred when importing an all-noninteger-dosage variant. VCF lines longer than 5 MB.

This can be run as a standalone command. We believe this was the cause of the VCF-import "File read failure" crashes reported over the last few months.

Cleaned up a few column names in --geno-counts and --hardy output. Left-normalization --normalize flag added. Fixed --glm linear-regression dosage handling bug in yesterday's build.

If you used a build from 14 Apr - 19 Jul to work with dosage data, the hardcalls may not have been thresholded correctly. Added debug-print code to support an ongoing multithread-VCF-dosage-import bug investigation if you are encountering mysterious "File read failure" errors during VCF import or "Malformed.

A1 column added to --adjust output in preparation for multiallelic variants. If you performed a whole-genome --glm run with the 9 Feb build or later, you should rerun with the latest build. However, single-chromosome and autosome-only --glm runs were unaffected by the bug. Operations like --pca which require decent allele frequencies now error out when frequencies are being estimated from less than 50 samples, unless you add the --bad-freqs flag.

Phased dosage support implemented. Sample missingness rate in exported. Clash of Clans. Subway Surfers. TubeMate 3. Google Play. The Best Black Friday deals. Bill Gates' favorite books of Hawkeye review. Xbox Game Pass Ultimate review. Windows Windows. Most Popular. New Releases. Desktop Enhancements. Networking Software. Trending from CNET. Download Now. Developer's Description By Sputnik Games. Plink is a fun game of chance and skill that's easy to learn.

Command reference table List of options List of output files Under development 5. Permutation procedures Basic permutation Adaptive permutation max T permutation Ranked permutation Gene-dropping Within-cluster Permuted phenotypes files Imputation beta Making reference set Basic association test Modifying parameters Imputing discrete calls Verbose output options Dosage data Input file formats Association analysis Outputting dosage data