Away Workshop (Philadelphia) 2014 Sep 18-19: Best Practices for Variant Calling with GATK
Eric Banks, Sheila Chandran and Geraldine Van der Auwera presented this workshop in Philadelphia, PA, upon invitation from the School of Medicine at UPenn.
This workshop covered all the core steps involved in calling variants with the GATK, using the “Best Practices” developed by the GATK team. The presentation materials describe why each step is essential to the calling process, what are the key operations performed on the data at each step, and how to use the GATK tools to get the most accurate and reliable results out of your dataset. This includes specific information about variant calling in RNAseq data and efficient analysis of cohorts.
The material was presented over two days, organized in the following modules:
- Data pre-processing: From FASTQ to analysis-ready BAM
- Variant Discovery: From BAM to analysis-ready VCF
This was complemented by a set of hands-on exercises aiming to teach basic GATK usage to new users.
The workshop materials are available at this link if you're viewing this post in the forum, or below if you are viewing the presentation page already.