Start Plinkomatic!
1. Overview
2. Main PLINK page
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PLINK-O-MATIC is an interactive, web-based documentation tool, designed to build commands for PLINK. By answering a series of simple questions, you will be shown
the command line needed to perform the actual analysis (that is, you will need PLINK installed
locally). The commands generated can either be copied into a terminal window or saved in a batch file.
The 6 screenshots below illustrate the steps in using PLINK-O-MATIC to build a command line.
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Answer some basic questions about the type of data you are using, and whether you want to
filter markers based on a number of criteria.
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Select the type of analysis, summary statistic or data management procedure you want from a decision
tree.
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Specify the names of the input and output files.
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Depending on your answers so far, some extra context-specific questions will appear at ths stage. In this
example, a panel allows the default thresholds for excluding SNPs and individuals based on
genotyping rate and allele frequency to be changed.
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Any errors will be flagged -- here, for example, the user forgot to specify a file name.
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When all the information has been collected, the PLINK command line is shown, and the
expected output files are listed.
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