Learn whole exome sequencing analysis with GATK best practices: alignment, variant calling, filtering, VEP annotation and clinical interpretation.
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Whole exome sequencing is one of the most widely used tests for finding disease-causing variants. This 15-day training teaches the complete WES workflow used in research and clinical genomics labs.
You go from raw FASTQ files to a clinical diagnosis: read QC with FastQC and fastp, BWA-MEM alignment, duplicate marking and base recalibration, exome coverage QC, GATK HaplotypeCaller with trio joint genotyping, variant filtering, annotation with Ensembl VEP, gnomAD and ClinVar, inheritance-based prioritisation, ACMG/AMP interpretation, IGV review and a clinical report. You practise on a family trio exome built on the real human chromosome 22 reference, ending with a mini project where you solve a rare disease case.
Learn from experienced educators and practitioners through practical, career-focused bioinformatics training.
12 answers about this course
Whole Exome Sequencing is a sequencing approach that focuses primarily on protein-coding regions of the genome, known as exons.
The training is suitable for biotechnology, bioinformatics, life science, genetics, genomics and related students, researchers and professionals.
No. The course starts with WES fundamentals and progressively moves toward practical data analysis.
Yes. Every class has a live hands-on part. You analyse a family trio exome on the real human chromosome 22 reference, using the same steps as a real clinical exome.
A laptop with 8 GB RAM and 5 GB free disk, running Linux, Mac, or Windows with WSL2. All software is free and is set up in the first classes.
FastQC, MultiQC, fastp, BWA-MEM, Samtools, GATK, mosdepth, BCFtools, Ensembl VEP and IGV, plus databases such as gnomAD, ClinVar and ClinGen.
Yes. The course covers SNP and indel calling with GATK HaplotypeCaller, joint genotyping of a trio, quality control and filtering.
Yes. You annotate variants with Ensembl VEP, gnomAD, ClinVar and prediction tools, then classify them with the ACMG/AMP guidelines.
Two assignments (a QC report and a variant QC report) and a mini project. A short practice quiz after each class helps you check your understanding; quiz scores do not count toward the certificate.
Yes. You receive a certificate when both assignments are approved and you submit the mini project.
Yes. You get the slides, practice data, ready-made scripts, a cheat sheet, an ACMG worksheet and a clinical report template.
Yes. You solve a rare disease case: filter the trio's variants, classify the top candidate with ACMG/AMP, write a clinical report and present it on Day 15.
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