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BioTech 79 | Variant Analysis

August 20, 2019 to August 23, 2019

Registration occurs on a first-come, first-served basis. The deadline for registration is one week before the first day of the course.  If you are unable to register before the deadline, please email: or call 301-496-7975 for space availability. 
NIH employees paying with the signed vendor copy of the SF-182 form, please email:

Register Now

Contract: SF-182

Next generation sequencing technologies have made genotyping a day to day research and diagnostic tool. Genotyping has come all the way from bench-to-bedside. Genetic variants are being used in personalized medicine to identify susceptibility genes, common disease variants and mutations relevant for diagnosis and therapy.

Participants will use popular open source tools and techniques necessary for analysing variants starting from raw data quality control. Apart from the regular analysis like alignment, variant calling and annotation, this training will walk through participants in several advanced variant analysis methods and techniques.

Who should attend:

  • Researchers and academics interested in learning the tools and methods to identify and study variants using techniques like DNA-Seq and other methods
  • Clinicians, researchers and academics interested in understanding/predicting the effect of mutations on the structure and function of a biological molecule for diagnostic and treatment potentials
  • Program administrators who are interested in getting a firsthand experience working with tools and techniques to understand variant analysis

Skill sets taught:

  1. NGS Basics, experimental design, data format
  2. Data quality control, preprocessing and alignment
  3. Germline variant calling
  4. Somatic variant calling
  5. Variant score recalibration and filtering
  6. Variant calling best practices
  7. Indels, structural and copy-number variation
  8. Cohort and population scale analysis
  9. Recombination, linkage, LOH, haplotype, allelic imbalance
  10. Variant annotation and association analysis
  11. Co-variation, causal variation, network analysis


  • Cloud-based Linux desktop
  • Training provided by active NIH researchers
  • Cookbook style bound manual for all exercises
  • Direct, after training support through exclusive forum membership
  • Continuing Education Credits

Workshops generally run from 9:00am - 5:00pm.​

Course Agenda:
Day 1

9 AM to 12 PM : Cloud computing setup & Linux basics

1 PM to 2.30 PM : Overview of Concepts in Variant Analysis (Presentation)

2.30 PM to 5 PM : Calling variants using GATK (Hands-on exercise)

Day 2

9 AM to 10 AM : Beyond SNPs: indels, copy number variants, and structural variants (Presentation)

10 AM to 12 PM : Working with indels (Hands-on exercise)

1 PM to 5 PM : Calling structural and copy-number variants (Hands-on exercise)

Day 3

9 AM to 10 AM : Identifying haplotypes and rare variants (Presentation)

10 AM to 12 PM : Identifying haplotypes, LOH, and de-novo variants in parent-offspring trios       (Hands-on)

1 PM to 2.30 PM : Phasing and imputation (Hands-on)

2.30 to 5 PM : Identifying rare variants          (Hands-on)

Day 4

9 AM to 10 AM : Variant annotation and association studies (Lecture)

10 AM to 12 PM : Single-locus association using Plink

1 to 4.45 PM : Network based variant analysis          

Note: Students will need to bring their own laptop to this program

Related BioTech Courses

BioTech 56: RNA-Sequencing

Comprehensive Binder
Contains all notes, protocols, and reference material needed. No additional books are required. 

Although no grades are given for courses, each participant will receive Continuing Education Units (CEUs) based on the number of contact hours.   One CEU is equal to ten contact hours.   Upon completion of this course each participant will receive a certificate, showing completion of the workshop and 2.8 CEUs.

General Training Rate
Discounted Training Rates
$695.00 - NIH Trainees (Fellows, PostDocs, PostBacs working at the NIH Campus)    
$895.00 - NIH Community (Working, Appointed, or Assigned to the NIH Campus)
$995.00 - Academia, Government, Military

Refund Policy                                                                                                             
100% tuition refund or 100% full workshop credit is available for registrations cancelled 14 or more days prior to the start of the workshop. 

50% tuition refund or 100% full workshop credit is available for registrations cancelled between 4 to 13 days prior to the start of the workshop. 

0% refund, 100% full workshop credit is available for registrations cancelled 
3 days or less prior to the start of the workshop.  

All cancellations must be received in writing via email to Ms. Carline Coote at

Cancellations received after hours are time marked for the following day.  

In regards to a full or partial refund or a full workshop credit, you must indicate which option you are selecting at the time of your written cancellation. 

All refund payments will be processed by the start of the initial workshop.

Suggested Accommodation:
A special rate is available to all BioTech Workshop attendees. This includes complimentary continental breakfast, guest room Wi-Fi and discounted $15 parking per night. Hotel is within walking distance of the training facility   Reservations can be made online, see below. 

DoubleTree by Hilton Bethesda - Washington DC


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