Okuzeka
Genetics & Biotechnology vocabulary · Bioinformatics

Variant calling

Meaning in genetics & biotechnology, with examples

nounCommon term

In genetics & biotechnology, variant calling means: The bioinformatics step that compares aligned reads with a reference genome to find where a sample's DNA differs, producing a list of variants.

In Turkish: varyant çağırma, varyant belirleme

How it is used

Used in genomics and clinical bioinformatics. A variant caller such as GATK produces a VCF file. People 'call variants', set quality filters and compare germline with somatic variant calling. Each variant found is a 'call', and a wrong one is a 'false positive call'.

Example sentences

  1. Variant calling was performed with GATK following best-practice guidelines.

  2. Low coverage in this region makes variant calling unreliable.

Common collocations

  • variant calling pipeline
  • germline variant calling
  • somatic variant calling
  • variant caller
  • call variants
  • alignmentArranging DNA, RNA or protein sequences side by side to find where they match, or placing sequencing reads in the right position on a reference genome.
  • variantA difference in a DNA sequence compared with a reference sequence. It is the neutral word used in clinical genetics, whether the change is harmful or harmless.
  • pipelineA series of connected software steps that process data automatically, for example from raw sequencing reads to a final list of annotated variants.
  • coverageThe average number of sequencing reads that cover each base of the target region. Higher coverage gives more confident results.
  • annotationAdding biological information to sequence data, for example marking where the genes are in a genome, or giving each variant its predicted effect and population frequency.

More terms: Bioinformatics

Practise with graded reading

Reading at the right level is the fastest way to make new words stick. Pick free English books by level: