Introduction to Variant Calling

Note: Some HBC workshops are taught in person and others are online via Zoom. Please take note for scheduling purposes!.

Workshop dates and times:

TBA: 9:30 AM - 12 PM

Instruction will be mostly learner-centric, requiring a time commitment between the workshop sessions!

Description:

This Introduction to Variant Analysis workshop is aimed at providing hands-on best practices for calling variants for paired normal/tumor datasets. Importantly, while this workshop focuses on calling variants in the context of paired tumor/normal samples, much of this workshop’s pipeline and discussion is adaptable to other types of variant calling applications. This workshop will demonstrate to participants how to take raw sequence reads and process them into a VCF file with annotated variants. Furthermore, the workshop ends with a tutorial for visualizing called variants within the Integrative Genomics Viewer (IGV) and creating figures using cBioPortal.

Prerequisites:

This is one of our advanced workshops, and assumes that users have a working knowledg of Shell and HPC or have attended the following Basic workshop offered by our training team in the last 6-8 months:

Shell for Bioinformatics (formerly called Introduction to command-line interface workshop)

There is an expectation of participants to have some/all of the following Shell/HPC knowledge:

Experience using a High-Performance Computing (HPC) cluster environment (e.g. O2 at HMS)
Navigating filesystems (changing directories, listing contents, full/relative paths, wildcards)
Creating, moving, copying, and removing files/directories
Searching files and redirection
Creating ‘for loops’ and small scripts
Creating long, advanced script

I am experienced using Shell/HPC but have not attended the HBC prerequisite workshop, can I still register?

Yes, please register and provide your Shell/HPC exerience on the form, and we’ll get back to you.

Who should attend?

Eligible* Harvard researchers who want to learn:

How to design an experiment to call variants
How to assess QC metrics at every step in the variant calling workflow
How to call variants within a paired normal/tumor context
How to visualize results within IGV
How to interact with cBioPortal and generate figures

Cost:

There is a non-refundable and non-transferable $65 registration fee for this advanced workshop*.

We will be accepting 25 participants on a first-come, first-served basis:

If you are one of the first 25 eligible* registrants, you will receive an email within 1 week with a link to pay the (non-refundable & non-transferable) $65 registration fee.
If you are not among the first 25 eligible* registrants, you will be added to the waitlist and notified when we open registration for the next iteration of this workshop.

NOTE: You will not have a reserved seat for this workshop until you pay the registration fee. Please make sure you pay within the time stated in that email, else you will lose your spot to someone on the waitlist.

*NOTE: HMS Graduate Students may receive waivers on registration fees. Please register and we’ll followup with you.

Registration:

Please make sure you take the following into account when signing up for the workshop:

Mandatory attendance for all four classes.
2-3 hours of reading and exercises from selected lessons before each workshop sessions.
Active participation during discussion sessions.

(Registration opens 2-3 weeks before the start of advanced workshops.)

Eligibility requirements:

^*To be eligible to attend this workshop you should fulfill at least one of the following criteria:

Harvard Medical School researcher in a lab on the Quad, with grants administered by HMS Gordon Hall
Harvard School of Dental Medicine researcher, with grants administered by HMS Gordon Hall
Graduate student at the Harvard Medical School
Researcher affiliated with the Dana-Farber / Harvard Cancer Center (DF/HCC)
Researcher at a Harvard-affiliated institution participating in HIV related research (CFAR).

If you are unsure of your eligibility, please register anyway and we will get back to you.

NOTE: We do not record our training sessions.

Questions?

Please email us at hbctraining@hsph.harvard.edu with any questions.