{"entity":{"id":"variant-calling","kind":"term","name":"Variant calling","aka":["variant calling","somatic variant calling","variant caller","variant callers","SNV calling","mutation calling"],"tldr":"Variant calling is the computational step that turns raw sequencing reads into a list of the DNA changes present in a tumour.","summary":"SNV calling from NGS data is any of a range of computational methods for identifying single nucleotide variants from next-generation sequencing results (Wikipedia); somatic callers such as Mutect2 compare tumour with matched normal reads. Calling is imperfect at low purity and low coverage, callers disagree, and the mutation lists TCGA released changed between pipeline versions. MutSigCV then asks which genes are mutated more often than the background rate, the standard driver-gene test.","asOf":"2026-09-24","wikipedia":"https://en.wikipedia.org/wiki/SNV_calling_from_NGS_data","links":[{"label":"Lawrence et al., Mutational heterogeneity in cancer and the search for new cancer-associated genes (MutSigCV, Nature 2013)","url":"https://doi.org/10.1038/nature12213"},{"label":"Wikipedia","url":"https://en.wikipedia.org/wiki/SNV_calling_from_NGS_data"}],"tags":["cansim-terms"],"related":["cancer-ai-vocabulary"],"cancers":[],"sections":[],"technologies":["wes-wgs","ngs-bioinformatics-software"],"targets":[],"drugs":[],"companies":[],"institutions":[],"pathways":[],"terms":["germline-vs-somatic","variant-effect-prediction","mutsig"],"trials":[],"people":[],"bottlenecks":[],"keyPapers":[],"journals":[],"dependsOn":[],"notes":["Listed in the CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme; CanSim page path /terms/variant-calling."],"provenance":{"editedBy":"OnCo CanSim terms wave (Wikipedia summaries, standards and project pages, GDC and FDA pages, Europe PMC)","editedOn":"2026-09-24","note":"CanSim terms map 1.0.0 (docs/onco/terms.json, generated 2026-09-24), CC BY 4.0, attribution: CanSim project, an open, public-data-first cancer foundation-model programme"},"category":"Genomics & genetics"},"route":"/terms/variant-calling/","neighbours":{"term":[{"id":"cancer-ai-vocabulary","kind":"term","name":"Cancer AI vocabulary (CanSim terms map)","route":"/terms/cancer-ai-vocabulary/"},{"id":"genome-builds","kind":"term","name":"Genome builds: GRCh38 versus hg19 (GRCh37)","route":"/terms/genome-builds/"},{"id":"germline-vs-somatic","kind":"term","name":"Germline vs somatic mutations","route":"/terms/germline-vs-somatic/"},{"id":"hgvs","kind":"term","name":"HGVS variant nomenclature","route":"/terms/hgvs/"},{"id":"mutsig","kind":"term","name":"MutSig (significantly mutated gene detection)","route":"/terms/mutsig/"},{"id":"somatic-mutations-wxs-wgs","kind":"term","name":"Somatic mutations from exome and genome sequencing (WXS, WGS)","route":"/terms/somatic-mutations-wxs-wgs/"},{"id":"variant-effect-prediction","kind":"term","name":"Variant effect prediction","route":"/terms/variant-effect-prediction/"}],"technology":[{"id":"ngs-bioinformatics-software","kind":"technology","name":"Clinical NGS bioinformatics and variant interpretation","route":"/technologies/ngs-bioinformatics-software/"},{"id":"wes-wgs","kind":"technology","name":"Whole-exome & whole-genome sequencing","route":"/technologies/wes-wgs/"}]}}