Variant Calling in Bacteria
One-Sentence Definition
Variant calling identifies SNPs and small indels by comparing sequencing reads mapped to a reference genome, producing the substitutions used for typing and resistance-mutation detection.
Simple Explanation
Line reads up against a reference and mark every letter that differs — those differences drive outbreak trees and some resistance calls.
Detailed Scientific Explanation
- Pipeline: map (BWA/minimap2) → sort/index → call (bcftools, FreeBayes, Snippy wrapper) → filter
- Haploid setting: bacteria are effectively haploid; heterozygous-looking calls suggest mixture or paralogy
- Filters: depth, mapping quality, strand bias, proximity to indels
- Recombination masking matters in species with high recombination before building trees
- Reference choice changes the SNP set — use a close reference or a pangenome-aware approach
Mechanism
Bayesian genotype likelihoods per site given read pileups and base qualities, then hard/soft filtering to control false positives.
Clinical Importance
- SNP distance thresholds inform whether two patient isolates plausibly share a transmission chain
- Chromosomal resistance mutations (e.g., gyrA, rpoB) are read directly from variants
Research Importance
- Within-host evolution, hypermutator detection, adaptation studies
Diagnostic Relevance
- Feeds Phylogenomics and Outbreak Typing and genotypic resistance prediction
AMR Relevance
- Point-mutation resistance is invisible to gene-presence-only tools — needs PointFinder-style logic (AMR Gene Databases)
Related MOCs
Active Recall Questions
- Why are heterozygous calls suspicious in a bacterial isolate?
- How does reference choice bias SNP counts?
- Which resistance types need variant calling rather than gene detection?