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Best Practices for Variant Calling with the GATK
By biogeek 1734 days ago
https://www.broadinstitute.org/partnerships/education/broade/best-practices-variant-calling-gatk-1
The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad’s Genome Analysis Toolkit (GATK) was version 3.3.
| 03/19/15 | Introduction to High-Throughput Sequencing data formats and methods | Joel Thibault | Video | |
| 03/19/15 | Introduction to the GATK | Geraldine Van der Auwera | Video | |
| 03/19/15 | Mapping, processing, and duplicate marking with Picard tools | Matt Sooknah | Video | |
| 03/19/15 | Mapping and processing RNAseq | Ami Levy-Moonshine | Video | |
| 03/19/15 | Indel realignment | Mark Fleharty | Video | |
| 03/19/15 | Base quality score recalibration | David Roazen | Video | |
| 03/19/15 | Introduction to variant discovery: calling cohorts | Louis Bergelson | Video | |
| 03/19/15 | Variant calling and joint genotyping | Sheila Chandran | Video | |
| 03/19/15 | Variant quality score recalibration | Bertrand Haas | Video | |
| 03/19/15 | Introduction to working with variants | Yossi Farjoun | Video | |
| 03/19/15 | Genotype refinement | Laura Gauthier | Video | |
| 03/19/15 | Annotation and variant evaluation | David Benjamin | Video |
