MPG Primer on sequencing and variant discovery pipelines
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.