Variant Analysis Workshop 2017

This workshop will include a rich collection of lectures and hands-on sessions, covering both theory and tools associated with command-line DNA variant analysis. Participants will explore experimental design, cost estimation, data generation, and analysis of DNA sequence data generated on the Illumina sequencing platform. Participants will explore software and protocols, create and modify workflows, and diagnose/treat problematic data utilizing high performance computing services. Exercises will be performed with provided datasets, using command-line interaction on the Genome Center Compute Cluster, which will be available to you for a week after the workshop, so you can continue to practice these skills.  We will also hold a follow-up Q&A session on Tuesday, Sept. 5.

Outline of Topics:

Monday Morning
Exercises: Intro to Command Line OR “Advanced” Command Line (Nik)

Monday Afternoon
Talk:  “What is Bioinformatics?”
Exercises: Running Jobs on the Cluster
Talk: “Intro to Sequencing”

Tuesday Morning
Talk/Exercises: Files and Filetypes for Genomes/Annotation [Fasta, fastq, gtf/gff, sam/bam, vcf]
Talk: “Experimental Design and Cost Estimation”

Tuesday Afternoon
Talk/Exercises: Quality check with fastqc, trimming for adapters and quality
Talk: “Philosophy of Preprocessing”

Wednesday Morning
Talk/Exercises: Sequence Alignment
Talk: “Genome Assembly and Annotation”

Wednesday Afternoon
Talk/Exercises: Variant Discovery Including GATK and Freebayes

Thursday Morning
Talk/Exercises: Variant effect annotation: snpEffect
Talk/Exercises: Filtering SNPs

Thursday Afternoon
Talk/Exercises:  SNP/CNV
Talk: “Cancer sequence analysis”

Friday Morning
Exercises:Intro to R

Friday Afternoon
Exercises: Variant analysis wth R
Talk: “GWAS”

Who should attend? … Prior course participants have included faculty, post docs, grad students, staff, and industry researchers.

What are the prerequisites? … There are no prerequisites other than familiarity with general biological concepts and an enthusiasm for learning bioinformatics data analysis. Some familiarity with the command-line and R is desirable.  However, we will dedicate time on the first day to bringing everyone up-to-speed to be able to run the commands needed during this workshop.

What do I need to bring? … You will need to bring your own laptop to use, have a recent version of Java installed, and an application that will allow you to ssh into a server (e.g. Putty for windows, or iTerm for Apple) as well as the ability to connect to the internet via wifi. Computational exercises will be performed on a remote server. We can help with setup early on in the workshop. If your department does not allow you to install software on the laptop you’ll be bringing, please contact us ahead of time.

Can I bring my own data? … We will provide experimental datasets for use during the workshop, as this helps to keep the workshop moving. There will be time, however, to discuss your own datasets and how you might work with them outside of the workshop.

How much does it cost? … The registration fee is $1,400 for UC and UC affiliates, $1,600 for other academic or non-profit participants and $2,000 for other participants. We accept credit cards, as well as UC Davis recharge accounts, for payment.  Registration fees include light breakfast, lunch, and snacks, but do not include dinner, lodging or parking fees.

Where is the workshop? … It will be held in Davis and will run from 9:30am to 4:30pm on the dates indicated. The specific location will be provided at a later date.

How do I apply? … All registration is “first-come, first-served”. There is no application process.  So, sign up as soon as possible to ensure your place in the workshop.

Where can I find more information, including your policies?  ... Go to our website (bioinformatics.ucdavis.edu/training/) and check out our FAQ and Policies.

Questions?

If you have any questions, please don’t hesitate to contact us at training.bioinformatics@ucdavis.edu