Variant Calling  
April 18,25 2016

In this workshop, practical issues related to calling SNP and indels from short reads alignments to a reference genome will be discussed, including the use of most popular short read aligners, such as BWA and Bowtie2, and variant-calling software with focus on the GATK pipeline. All topics will be illustrated with hands-on exercises performed by participants at their own pace on the assigned BioHPC Lab computers, during the workshop or at home, using the provided step-by-step instructions.

Workshop attendees are encouraged to bring laptop computers to serve as terminals to the Bioinformatics Facility's BioHPC Lab workstations where the actual computations will take place. Our workstations run Linux operating system, so if you are going to use our machines and are new to Linux computing environment you may want to attend our free  workshops "Introduction to BioHPC Lab" and "Linux for Biologists". You can also use both workshop materials posted online to refresh your Linux skills:

Linux for Biologists Part 1   Linux for Biologists Part 2

Registration fee is $100. Bioinformatics Facility is organizing 6 workshops in the Spring 2016 - if you'd like to register for all of them at a reduced rate please go to this page.

Access to BioHPC Lab workstations requires a Lab account. If you do not yet have an account on BioHPC Lab system, we will create one for you. Also, we will assign a machine for you to work on during and after the workshop.

Machine allocations are posted here.

Workshop Outline
Session 1 4/18/2016 3:30:00 PM 655 Rhodes Hall
Session 2 4/25/2016 3:30:00 PM 655 Rhodes Hall
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