DNASeq III Practical

Continuing with the HTSLIB mapping to variant workflow, now we'll start using GATK.

• GATK
• GATK Quickstart
• GATK Best Practices

GATK has much better workflows for variant calling and you should use them! We just don't have enough lab time to get quite that detailed, but you should see enough of the process to be able to expand to the full recommended workflow if needed.