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Quick index search. What’s new? Methods paper. Usage questions should be sent to the plink2-users Google group , not Christopher’s email. Source code, compilation instructions, and the like are on the developer page. 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. This may make some commands a bit slower.
You can remove this restriction with –native. The bug was pretty obvious if you were affected by it the. In the development build, –dfam consistently errors out with an appropriate message, instead of possibly segfaulting, when no valid cases are present. Scientific notation can now be used for command-line integer parameters. Fixed –R memory leak. If you used –merge-equal-pos with.
Fixed an inaccuracy in –adjust’s handling of very small p-values. This bug was much more likely to trigger if the first. Why was this discovered now, more than 2. Fixed –logistic bug that could cause spurious NA results. Improved –score compatibility with v1. Minor statistical phasing bugfix. PLINK 2. Fixed «–model gen» permutation testing bug. Fixed use-after-free bug in extra chromosome name cleanup code.
Fix minor backward compatibility break. Minor –test-missing permutation bugfix. If you used adaptive permutation with –logistic in the past, we recommend that you redo the run with the latest build.
Several –indep-pairphase bugfixes. Errors and warnings are now printed to stderr instead of stdout yes, this is overdue. Fixed –homozyg. Revised heterozygous haploid warning to be clearer. Update, 15 June: you can now use the –mds-plot ‘eigendecomp’ modifier in the development build to request the eigendecomposition algorithm, with the centering bug fixed. It does have the virtue of being several times faster than SVD. Missing genotype calls at otherwise monomorphic loci in multichar-allele.
QFAM test closed for repairs. Fixed a set-handling bug that could affect sets containing the dataset’s last variant. Compact Genomes phase 1 data files posted on the resources page.
But if you used the UNAFF rows in the –hardy report for anything, you should rerun –hardy with the latest build. Some numeric stability improvements for small p-values. UNADJ column values are now correct in «–adjust gc» reports.
Single-precision binary matrix output e. Binary –distance output bugfix. Merger no longer scrambles centimorgan coordinates. If you have used –biallelic-only without ‘strict’ on VCF files with triallelic variants, we strongly recommend rerunning the operation with the latest build.
Presence of nonnumeric phenotype strings e. Malformed files generated by some old merges no longer cause segfaults. Most merges were unaffected, but better safe than sorry. Handling of this case may be configurable in the future, stay tuned. Corrected misnamed –filter-attrib[-indiv] flags to –attrib[-indiv], fixed a positive matching bug, and added support for gzipped attribute files.
Merger now provides an informative error message when given an sample-major. Within-cluster permutation bugfix. Malformed input error messages now include line numbers. Basic parent-of-origin test implemented. Basic –score implemention. Markers with identical bp coordinates no longer cause 1. D-prime computations «–r2 dprime», –ld, –blocks, –clump involving variants on the X chromosome now appropriately downweight males relative to females.
We hope we were the only actual victims of this. VCF allele code Nazi now just issues a warning, since some pipelines actually depend on violating the official spec. VCF ‘N’ reference allele now handled in a saner manner converted to and back from missing. VCF generator now forces the A2 reference allele to always be known, and outputs ‘. LD-based result clumping –clump is now supported. This multithread efficiency issue will be solved in the near future.
Also see the major bugfix above. Optional ‘chr’ chromosome prefixes may now be partly or entirely capitalized. Gzipped and binary Oxford genotype files can now be directly imported.
Fixed contig name handling bug which slipped into 23 Jan builds. Hardy-Weinberg and Fisher’s exact tests now support mid-p adjustments. Proper handling of ambiguous sex codes. Y chromosome «nonmissing nonmale genotypes» warning no longer gets sexes backwards oops. Mitochondrial DNA no longer required to be haploid though there are no plans to support full polyploidy.
Cluster permutation and –covar-name range handling bugfixes. Basic –test-missing. Fixed a bug which sometimes came up when using –ibs-test or association analysis commands while filtering out samples.
Also fixed the –distance segfault introduced in the 18 Dec build; sorry about that. A bit of dead wood trimmed to make way for better implementations –regress-pcs, dosage distance calculator ; let us know if you want those functions to return sooner rather than later. Add check for matching input and output filenames when using –rel-cutoff in batch mode.
Cluster membership filters added –keep-clusters, –keep-cluster-names, –remove-clusters, –remove-cluster-names. Nonautosomal chromosome filtering bugfix. Unprecedented speed Thanks to heavy use of bitwise operators, sequential memory access patterns, multithreading, and higher-level algorithmic improvements, PLINK 1. See the credits page for a partial list of people to thank. 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.
Nearly unlimited scale The main genomic data matrix no longer has to fit in RAM, so bleeding-edge datasets containing millions of variant calls from exome- or whole-genome sequencing of tens of thousands of samples can be processed on ordinary desktops and this processing will usually complete in a reasonable amount of time. In addition, several key sample x sample and variant x variant matrix computations including the GRM mentioned below can be cleanly split across computing clusters or serially handled in manageable chunks by a single computer.
There are other additions here and there, such as cluster-based filters which might make a few population geneticists’ lives easier, and a coordinate-descent LASSO. PLINK’s primary job is management and analysis of position-based SNP-like data for thousands of samples, and it is optimized for this setting.
Here are a few things PLINK will probably never be able to do, since they are serious jobs best handled with fundamentally different data structures than the ones PLINK is built around. We are primarily interested in the following three types of feedback during the current testing phase:. Comments should generally be made in the plink2-users Google group. PLINK 1. File formats Introduction, downloads S: 16 Apr b6. Identity-by-descent –genome –homozyg Distributed computation Command-line help Miscellaneous Tabs vs.
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Missing genotype calls at otherwise monomorphic loci in multichar-allele. QFAM test closed for repairs. Fixed a set-handling bug that could affect sets containing the dataset’s last variant.
Compact Genomes phase 1 data files posted on the resources page. But if you used the UNAFF rows in the –hardy report for anything, you should rerun –hardy with the latest build. Some numeric stability improvements for small p-values. UNADJ column values are now correct in «–adjust gc» reports. Single-precision binary matrix output e. Binary –distance output bugfix. Merger no longer scrambles centimorgan coordinates. If you have used –biallelic-only without ‘strict’ on VCF files with triallelic variants, we strongly recommend rerunning the operation with the latest build.
Presence of nonnumeric phenotype strings e. Malformed files generated by some old merges no longer cause segfaults. Most merges were unaffected, but better safe than sorry. Handling of this case may be configurable in the future, stay tuned. Corrected misnamed –filter-attrib[-indiv] flags to –attrib[-indiv], fixed a positive matching bug, and added support for gzipped attribute files. Merger now provides an informative error message when given an sample-major.
Within-cluster permutation bugfix. If none of the previous three troubleshooting steps have resolved your issue, you can try a more aggressive approach Note: Not recommended for amateur PC users by downloading and replacing your appropriate Plink. Please follow the steps below to download and properly replace you file:.
If this final step has failed and you’re still encountering the error, you’re only remaining option is to do a clean installation of Windows To avoid data loss, you must be sure that you have backed-up all of your important documents, pictures, software installers, and other personal data before beginning the process. If you are not currently backing up your data, you need to do so immediately. The installer’s task is to ensure that all correct verifications have been made before installing and placing Plink.
An incorrectly installed EXE file may create system instability and could cause your program or operating system to stop functioning altogether. Proceed with caution. You are downloading trial software. Subscription auto-renews at the end of the term Learn more.
How to Download Plink. Zipped HTML: puttydoc. Plain text: puttydoc. Unix source archive. Compiled executable files for bit Windows on Arm.
We’ve had reports that these can be useful on Windows IoT Core. If your original file is just corrupted but not lost, then please check the version number of your files. Method: Click your original file, and then click on the right key to select «Properties» from the pop-up menu, you can see the version number of the files 3.
If your operating system is bit, you must download bit files, because bit programs are unable to run in the bit operating system. There is a special case that, the operating system is a bit system, but you are not sure whether the program is bit or bit. If you encounter this situation, check the file path to see whether there are any other files located in.
If yes, please check the properties of these files, and you will know if the file you need is bit or bit. Therefore, you could be sitting at one PC and giving commands for others thanks to these protocols via the standard client and server principle.
At the same time, the application allows you to connect to a specific port and packs several options that can only be applied to an SSH connection, such as X11 forwarding, serial configuration, compression or Dynamic SOCKS-based port forwarding, for instance.
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