Process Description

PLINK Binary Input Engine

The PLINK Binary Input Engine imports a PLINK (Purcell et al., 2007) binary file (.bed) and associated text files (.bim and .fam) into a SAS data set containing the marker genotypes and traits, and a SAS data set containing annotation (marker map) information.

What do I need?

Three files are needed to run this process:

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The PED file in binary format (.bed). The SNP_984_sample1000.bed file included in the SNP984_Sample1000 sample setting for this process serves as an example.

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The extended map text file (.bim). The SNP_984_sample1000.bim file serves as an example and is partially shown below.

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The .fam text file. The SNP_984_sample1000.fam file serves as an example and is partially shown below.

All files included in the SNP984_Sample1000 sample setting for this process were downloaded from http://www.hsph.harvard.edu/research/skat/download/. For additional details about the required file formats, please refer to the following links:

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http://pngu.mgh.harvard.edu/~purcell/plink/

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http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml

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http://pngu.mgh.harvard.edu/~purcell/plink/binary.shtml

For detailed information about the files and data sets used or created by JMP Genomics software, see Files and Data Sets.

Output/Results

The output data sets generated by this process are listed in a Results window. Refer to the PLINK Binary Input Engine output documentation for detailed descriptions.