28 April 2022 - 10am
via zoom
Workshops
Variant calling using GATK4 command line workflow
Workshop date/time (Melbourne time): Thursday 28th April 10-2pm
EOI deadline: 5pm Thursday 14th April
Successful applicants notified: Thursday 21st April
Workshop outline
This workshop aims to introduce participants to variant calling using command line applications. The material follows the GATK variant calling best practices workflow and provides an introduction to tools, datatypes and file formats associated with variant calling. The workshop will use a test llumina sequencing dataset to progress through the workflow from aligning sequencing reads to a reference genome before applying the GATK best practices workflow to call genetic variants (SNVs and Indels) in test data.
Tools used
- BWA
- Samtools
- GATK4
- picard
- bcftools
- jigv
- Align reads to a reference genome
- Call simple variants using the GATK best practices workflow
- Be introduced to SAM/BAM and VCF file formats
- Follow instruction to run command line applications