Content Comparison

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

We're going to assume that You can start this tutorial two ways

1. If 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 fromfrom doing the previous tutorials, then you can use it for this tutorial.

cd $SCRATCH/intro_to_mapping

If you do not have the results, you can copy them some "canned" ones that we provide using these commands. Remove any existing intro_to_mapping directory in your $SCRATCH space before running these commands, if you have one.

cds
cp -r /corral-repl/utexas/BioITeam/ngs_course/intro_to_mapping/data intro_to_mapping
cd intro_to_mapping
cp -r /corral-repl/utexas/BioITeam/ngs_course/intro_to_mapping/samtools_* .
cp -r /corral-repl/utexas/BioITeam/ngs_course/intro_to_mapping/comparison .

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