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.

(BP3.0) Suggested preliminary analyses

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 5,276Administrator, GSA Member admin
edited December 2013 in Methods and Workflows

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

Once you have generated and filtered your callset according to our recommendations, you have several options for evaluating and refining the variant and genotype calls further, before moving on with your study. We do not provide comprehensive guidelines for this step because different studies will have different requirements, but we do provide tools and general advice.

The main options available through GATK are:

  • Genotype Refinement
  • Functional Annotation
  • Variant Evaluation

Some of the tools involved in those processes (such as SnpEff and BEAGLE) are third-party tools that are not part of GATK. We recommend those specific tools because we are most familiar with them, but there may be alternative software that would work just as well or even better with your particular data. Also, please understand that we cannot provide support for those tools; if you have any problems with them we suggest you seek out the corresponding documentation form the tool project websites, and contact their developers with any questions you may have.

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Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

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