Sequence Alignment and Variant Calling using YCGA Pipeline.
Sequence Alignment and Variant Calling using YCGA Pipeline. In-Person
In this class, we will review the basic concepts of sequencing alignment and variant calling. Variant calling is a process used to identify variations in the DNA sequence. We will focus on germline short variant discovery (SNVs and indels) from Whole Exome Sequencing (WES) or Whole Genome Sequencing (WGS) data. This class includes hands-on practice using the Open OnDemand platform to set up and use the YCGA’s germline and somatic variant calling pipelines. We will work with a WES trio in which the proband is affected by a rare disease, with the goal of finding the disease-causing gene. After this practice, you should be able to run your own data using the YCGA pipelines.
Requirements:
- Laptop with internet access
- For those less familiar with command-line interfaces, complete in advance the Codecademy lessons for “Learn Command Line” (free): https://www.codecademy.com/enrolled/courses/learn-the-command-line
- For those not familiar with Open On Demand please review the following video: https://research.computing.yale.edu/training/hpc-series/introduction-open-ondemand-ood
- Date:
- Tuesday, November 19, 2024
- Time:
- 9:00am - 12:00pm
- Time Zone:
- Eastern Time - US & Canada (change)
- Location:
- C-103, SHM, 333 Cedar St, New Haven, 06510
- Campus:
- Medical School
- Categories:
- Bioinformatics
