I am trying to get SNPs and indels from a bowtie 2 on Illumina reads matched to the sinorhizobium meliloti (RM1021) genome using MPileup. When setting up the MPileup it asks for a reference genome. I can not find the sinorhizobium meliloti genome in the list of options. Is my genome in the list,but I don't know what it is called? Is there a way to add my reference genome to the list?
Tool name: MPileup
Tool version: 0.0.1
Tool ID: toolshed.g2.bx.psu.edu/repos/devteam/samtools_mpileup/samtools_mpileup/0.0.1
ToolShed URL: http://toolshed.g2.bx.psu.edu/view/devteam/samtools_mpileup