Variant Analysis Workshop 2020

Listed topics are preliminary and subject to change. For documentation from previous workshops, visit http://bioinformatics.ucdavis.edu/training/documentation/.

A preliminary agenda for the week includes:

Introductory materials

• Introduction to command line
• Running jobs on the cluster
• Introduction to R and RStudio

Data Reduction - sequence analysis

• Files and filetypes for genomes and annotation: fasta, fastq, gtf/gff, sam/bam, and vcf
• Quality checking and preprocessing
• Sequence alignment

Data Reduction - variant calling

• Variant discovery, including GATK and Freebayes (maybe deep variant)
• Variant effect annotation: snpEffect
• Copy Number, Structural Variants
• Filtering variants

Data Analysis

• Variant analysis with R
• Genome Wide Association Studies (GWAS Analysis)

Special Topic talks

• Introduction to Bioinformatics (talk)
• Experimental design and cost estimation (talk)
• Introduction to High Throughput Technologies (talk)

The pace of each workshop highly dependant upon the skill level of attendees and so is slightly different each time. Sorry but we cannot schedule topics/part down the day/hour.