Introduction to Variant Calling (2024)
Note: In 2024, some workshops will be taught in person and others will be online via Zoom.
IN-PERSON Workshop dates and times:
Location: Longwood Medical Area
Tuesday, May 28, 2024: 9:30 AM - 12 PM
Friday, May 31, 2024: 9:30 AM - 12 PM
Tuesday, June 4, 2024: 9:30 AM - 12 PM
Friday, June 7, 2024: 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 requires registants to have attended the following Basic workshop offered by our training team in the last 6-8 months:
I am fluent in command-line and already use HMS-RC’s O2 cluster but have not attended the HBC prerequisite workshop, can I still register?
Yes, you can register AND please do the following:
- Complete the registration first
- Then email us directly at hbctraining@hsph.harvard.edu with a detailed description of your knowledge/experience in command-line interface and HPC. Failure to do this step may prevent you from being accepted into this advanced workshop.
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.
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.
(Please check the eligibility requirements prior to registering)
NOTE: We do not record our training sessions.
Questions?
Please email us at hbctraining@hsph.harvard.edu with any questions.