GATK analysis using Bam files after BWA alignment
I need to perform GATK analyis on my Maize chloroplast samplea. I already generated bam files after aligning data from my samples with reference maize chloroplast genome. My objective is to look foa a single base changes in different samples.
Please provide me the steps to perform the analysis on fire cloud. I do not have any programming skills, so please let me know how I can import GATK analysis files from other workspaces or methods.