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.

(BP3.3) Variant Evaluation

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,293Administrator, GSA Member admin

This article is part of the Best Practices workflow documentation. See http://www.broadinstitute.org/gatk/guide/best-practices for the full workflow.

Whether your callset is big or small, you'll probably need to evaluate it against others, or query it to identify the variants that are relevant to your work. The GATK offers multiple ways to perform these tasks efficiently at scale. For this step, we do not provide a standardized workflow because it depends too much on the needs of individual projects. However, our documentation provides a number of concrete examples of what you can do with these tools.

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

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