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MPG Primer on sequencing and variant discovery pipelines

Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie

Geraldine Van der Auwera presented this talk as part of the Broad Institute's Medical and Population Genetics (MPG) Primers series.

This talk provides a high-level overview of the workflow for performing variant discovery on high-throughput sequencing data, as described in the GATK Best Practices and implemented in the Broad's production pipelines.

The following points emphasized in this presentation are:

  • Informational content of data file formats and flow of information throughout the pipeline
  • Concepts involved in the data transformations (processing steps and analysis methods)
  • Motivation and key mechanics of the GVCF workflow for scalable joint variant discovery
  • Relation of the GATK Best Practices to the Broad's production pipeline implementation

The presentation slide deck is available at this link.

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