Bug Bulletin: we have identified a bug that affects indexing when producing gzipped VCFs. This will be fixed in the upcoming 3.2 release; in the meantime you need to reindex gzipped VCFs using Tabix.

BroadE Workshop 2012 Dec 4-5: Best Practices for Variant Calling with the GATK

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,293Administrator, GSA Member admin
edited January 2013 in Events

This workshop covered the core steps involved in calling variants with the Broad’s Genome Analysis Toolkit, using the “Best Practices” developed by the GATK team. View the workshop materials to learn 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.

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Geraldine Van der Auwera, PhD

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