Processes | Import | Call Variants with SAMtools

Call Variants with SAMtools
This process uses SAMtools/BCFtools (version 0.1.12) to call SNPs/INDELs from BAM files, generating VCF (variant call format) files as output. You can then import the VCF files into a SAS data set.
Important: Before running this process, you must download SAMtools from and save the executable files under the folder C:\Program Files\SASHome\JMPGenomics\13\Genomics\ThirdPartyAnnotation\NextGen.
Note: This process is considered experimental.
What do I need?
To run this process, you need the following input data:
One or more Files for Variants Call. These must be Compressed Binary Sequence Alignment Map (BAM) files with extension “.bam”. An example is the NA18507_maq.bam file (not shown), found in the JMP Genomics LifeSciences\Sample Data\Next-Gen\ folder.
A Reference File. This file must contain a FASTA-formatted Reference Sequence, and have an extension of “.fa”. An example is the NA18507.fa file, found in the JMP Genomics LifeSciences\Sample Data\Next-Gen\ folder, and 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.
The output data sets generated by this process are listed in a Variants Call Message window. Refer to the Call Variants with SAMtools output documentation for detailed descriptions.