VCF Input Engine

This process imports VCF (variant call format) version 4.0 or 4.1 files¹ into (tall) SAS data sets, with a separate output data set per chromosome if there are more than one million loci in a file. Additional wide SAS data sets can be requested.

Important: Before running this process, you must navigate to the C:\Program Files\SASHome\JMPGenomics\13\Genomics\ThirdPartyAnnotation\ folder and create a new folder and name it NextGen. You must then download SAMtools version 0.1.12 (for Windows) from https://sourceforge.net/projects/samtools/files/samtools/0.1.12/ and save the executable files in the newly created NextGen folder.

What do I need?

You must specify one or more VCF files, which must all be located in the same folder.

For example, the trio.ychr.vcf file, found in the LifeSciences\Sample Data\Genetics\ folder, can be specified. It is shown below.

For detailed information about the files and data sets used or created by JMP Life Sciences 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 VCF Input Engine output documentation for detailed descriptions.

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See VCF (Variant Call Format) version 4.0 for more information about these file formats.