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Phase 2 — Core Bioinformatics
Module 09

Variant Calling

Call SNPs and indels from sequencing data — the foundation of GWAS, population genomics, and precision medicine. Follow GATK best practices, understand VCF format, and filter variants correctly.

Weeks 13–14Timeline
~14 hrsStudy time
FREEAlways
Start Lesson 1 → View in curriculum →
What you'll learn

Topics covered in this module

GATK
HaplotypeCaller
VCF format
BCFtools
BQSR
SnpEff

📋 Not sure where this fits? Module 09 is part of the full bioinformatics curriculum — a structured 42-week learning path from Bash to single-cell RNA-seq.

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Lessons

13 lessons in this module

01What is Variant Calling? Concepts & OverviewLive →
02Setting Up GATK, samtools & Reference GenomeComing soon
03Read Alignment with BWA-MEMComing soon
04Sorting, Indexing & Marking DuplicatesComing soon
05Base Quality Score Recalibration (BQSR)Coming soon
06HaplotypeCaller — Calling VariantsComing soon
07Joint Genotyping with GenomicsDBImport & GenotypeGVCFsComing soon
08Variant Filtration — VQSR & Hard FiltersComing soon
09Annotating Variants with ANNOVAR / SnpEffComing soon
10Filtering & Interpreting VCF FilesComing soon
11Structural Variants & CNV CallingComing soon
12Plant Genome Variant Calling (Sorghum/Rice case study)Coming soon
13Capstone: End-to-End GATK Pipeline ScriptComing soon

Lesson 1 is live.

Lesson 1 — What is Variant Calling? Concepts & Overview is ready to read now. The remaining 12 lessons are being built, each with exercises, datasets, and a GitHub repository you push as proof of skill. Sign up to be notified as they go live.

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Module 09 of 31