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This course introduces pipelines for processing and genotyping 2bRAD data.

It includes a GATK pipeline (requires a reference genome) and a de novo pipeline (does not require reference genome).

The course is divided into sections with 'Walkthoughs'. These are text files with commands and comments on how to acquire and analyze the data. In each walkthrough the instructions are commented out and the commands are not, so its easy to copy and paste them into the terminal.

Example:

#save the text '2bRAD' to a file called data.txt:

echo '2bRAD' > data.txt

 

Walkthroughs:

  1. Downloading Course Data
  2. Setting Up Scripts
  3. Setting Up Reference Genome
  4. Preparing Reads
  5. Genotyping With GATK
  6. de novo Genotyping with Matz pipeline

 

Additional Files:

  1. Modules Paths and Variables
  2. Sequence Alignment:Map Format Specifications.pdf
  3. The Variant Call Format Specifications.pdf
  4. plot_tranche_results.R
  5. Notes on Matz de novo pipeline
  6. Slides
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