In this tutorial, we're going to view the aligned reads and variants that we called in the past two lessons in the Integrated Genomics Viewer from the Broad Center. You'll need the output from Introduction to mapping (bowtie, BWA) and Introduction to variant calling (Samtools).
Getting situated
Create a fresh directory for this tutorial. We're going to assume that it's inside of the you have an introduction_to_mapping directory, and that you have existing results in those subdirectories. If not, see us and we can tell you where to copy "canned" results from.
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