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\JMP\10\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 .
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.