Download Plink2 _TOP_
Tessa Frabott
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. (What's new?) (Credits.) (Methods paper.) (Usage questions should be sent to the plink2-users Google group, not Christopher's email.)
PLINK 2.0 alpha was developed by Christopher Chang, with support from GRAIL, LLC and Human Longevity, Inc., and substantial input from Stanford's Department of Biomedical Data Science. (More detailed credits.) (Usage questions should be sent to the plink2-users Google group, not Christopher's email.)
I have been using plink 1.9 before and today downloaded the MacOS 64-bit^2 version of plink2. I made sure that I was in the same directory as where I stored plink2.exec but I still could not get plink2 to operate on terminal. When I input ./plink2 on terminal, the output was a bunch of command introduction for plink2, which was expected, but when I input plink2, it keeps saying "command not found". What am I doing wrong? I have tried searching unfortunately I have yet to see another person with the same problem.
One of the key advantages of plink2 is its pgen/pvar/psam format that efficiently stores large-scale genotype dataset. As a part of plink2 software, there is an R binding called pgenlibr that allows us to read genotype data from pgen file.
One can use plink2 binary software to convert your genetic dataset into this format. For example, the following --make-pgen (link to reference) command will convert your input.vcf file into binary_fileset.pgen,pvar,psam. Many other input formats are also supported in plink2.
plink2 is:plink expects as input the data from SNP (single nucleotide polymorphism)chips of many individuals and their phenotypical description of a disease.It finds associations of single or pairs of DNA variations with a phenotypeand can retrieve SNP annotation from an online source.SNPs can evaluated individually or as pairs for their association with thedisease phenotypes. The joint investigation of copy number variations issupported. A variety of statistical tests have been implemented.
plink2 is a comprehensive update of plink and plink1.9 with new algorithmsand new methods, faster and less memory consumer than the first plink.There are three methods to install plink2 on Ubuntu 22.04. We can use apt-get, apt and aptitude. In the following sections we will describe each method. You can choose one of them.
Update apt database with apt-get using the following command.sudo apt-get updateAfter updating apt database, We can install plink2 using apt-get by running the following command:sudo apt-get -y install plink2Install plink2 Using aptUpdate apt database with apt using the following command.sudo apt updateAfter updating apt database, We can install plink2 using apt by running the following command:sudo apt -y install plink2Install plink2 Using aptitudeIf you want to follow this method, you might need to install aptitude first since aptitude is usually not installed by default on Ubuntu. Update apt database with aptitude using the following command.
To uninstall only the plink2 package we can use the following command:sudo apt-get remove plink2Uninstall plink2 And Its DependenciesTo uninstall plink2 and its dependencies that are no longer needed by Ubuntu 22.04, we can use the command below:sudo apt-get -y autoremove plink2Remove plink2 Configurations and DataTo remove plink2 configuration and data from Ubuntu 22.04 we can use the following command:
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