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 http://samtools.sourceforge.net/ and save the executable files under the folder C:\Program Files\SASHome\JMPGenomics\12\Genomics\ThirdPartyAnnotation\.
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.
Output/Results
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.