No two genomes are exactly alike. Variant calling is the process of finding the differences between a sample and a reference genome, such as single nucleotide changes (SNPs) and small insertions and deletions (indels). It is behind work in medicine, population genetics, and microbial genomics.
You'll start with the VCF file, the standard format for storing variants. You'll learn what its header, columns, and genotype fields mean, and how it differs from a gVCF.
Then you'll follow a full workflow from raw reads to variants: aligning reads with BWA, then calling variants with GATK or with Samtools and BCFtools. This builds directly on the read quality control from the previous module. Once you've finished, move on to Transcriptomics & RNA-seq.
A detailed workflow for calling SNPs and indels from whole genome sequencing data, following GATK best practices from raw reads to a VCF file.
A hands-on lecture on calling variants (SNPs and indels) with Samtools and BCFtools.
A workshop using Broad Institute materials to teach variant calling with GATK, aimed at people with no prior experience.