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\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.

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.