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Day 6: DNA Resequencing and Variant Calling

Day 6: DNA Resequencing and Variant Calling

Welcome to Day 6 of the Short-Read Sequencing Analysis Workshop.The videos for day 6 will go over a resequencing pipeline using Bowtie2 and the GATK Toolkit for vairant calling. The two videos will show you how to work with both single-end and paired-end reads, and how to work with both artificial/model data and real Illumina sequencing data.

 

Videos for Day 6

Video 1: Introduction to Resequencing (4:43)  This first video gives some general background on resequencing pipelines, what can be learned, and important considerations.

Video 2: Pipeline for Variant Calling with GATK (7:09)  The second video shows how GATK can be used to pre-process mapping results and call SNPs and indels.

Video 3: Post-Processing Variant Results (6:51)  This last video introduces methods for variant filtering and variant annotation using SnpEff.

 

Files for Day 6

In-class slides for Day 6

Homework for Day 6 

 

Additional Resources

GATK Guide This guide can help you find out useful information about all of the GATK tools available as well as links to GATK "Best Practices" for DNA and RNA sequencing analysis (** please note GATK Toolkit is free for academic use, there is a fee for a commercial license)

SnpEff website  This site has the installation files, as well as manuals and documentation on how to use the program

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