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Variant Calling

Definition
AI-generated

Variant calling is the process of identifying sequence differences such as SNVs and indels from aligned sequencing reads relative to a reference genome.

Topics
Sequencing and omics tech
Related
Base Quality Score Recalibration (BQSR) Binary Alignment/Map (BAM) Coverage

Why it matters in GWAS

The quality of variant calling determines which variants enter downstream association analyses, burden tests, and reference panels for imputation.

Example usage

"Joint variant calling was performed across all sequenced samples before sample and variant QC."

Base Quality Score Recalibration (BQSR) Binary Alignment/Map (BAM) Coverage Genome Analysis Toolkit (GATK) HaplotypeCaller Read Variant Annotation Whole-Exome Sequencing (WES) Whole-Genome Sequencing (WGS)
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Koboldt DC. (2020). Best practices for variant calling in clinical and population sequencing. Nat Methods.
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