Call Variants with SAMtools

Running this process for the humasn_b36_seq2 sample setting generates the Variants Call Message window shown below. Refer to the Call Variants with SAMtools process description for more information.

The Variants Call Message window contains the following elements:

Output Files

This process generates the following file(s):

•	VCF File(s) : The variant call format 4.1 files 1 can be imported into (tall) SAS data sets.

Launch Follow-Up Process

•	Import VCF Files : Click Import VCF Files to launch the VCF Input Engine process, with the generated output files from the Variants Call with Samtools process automatically specified as files to import.

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