Until then, BEAGLE 3.3 should be more accurate than PLINK for case/control haplotype association.Ħ: Free database software handles these operations in a more flexible and powerful manner.ħ: Just use gzip/ gunzip for this. Future PLINK versions will be able to import phase and dosage information emitted by other programs the haplotype association commands will be reintroduced when that functionality is in place. We recommend migrating away from PLINK 1 here, but if that's not practical, keep a permanent copy of the PLINK 1.07 binary around and modify the relevant lines of your scripts to explicitly refer to it.ģ: We believe this now has almost no practical value, since the file format it expects is too different from VCF.Ĥ: This was not fully developed in PLINK 1.07, and has been superseded by other IBD analysis packages.ĥ: PLINK's haplotype phasing and imputation algorithms are obsolete.

red flags will not be supported by the final 1.90 release.

You're more than welcome to try the new implementations just make sure to check some of your results against PLINK 1.07 if you do so.

green flags are supported by the latest development build.

The following documented PLINK 1.07 flags are not supported by 1.90 beta 7:Ĭontinue using PLINK 1.07 for most of these operations. Source code, compilation instructions, and the like are on the developer page.

ģ: You need to have Rosetta 2 installed to run this on M1 Macs. ( What's new?) ( Credits.) ( Methods paper.) (Usage questions should be sent to the plink2-users Google group, not Christopher's email.) Binary downloadsġ: Solaris is no longer explicitly supported, but it should be able to run the Linux binaries.Ģ: These are just mirrors of the binaries posted at. This is a comprehensive update to Shaun Purcell's PLINK command-line program, developed by Christopher Chang with support from the NIH-NIDDK's Laboratory of Biological Modeling, the Purcell Lab, and others.

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