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Variant calling is the computational step that turns raw sequencing reads into a list of the DNA changes present in a tumour.
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.
Showing the technology this term belongs to: Whole-exome & whole-genome sequencing.
Shares Genome builds: GRCh38 versus hg19 (GRCh37), Clinical NGS bioinformatics and variant interpretation, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares MutSig (significantly mutated gene detection), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Genome builds: GRCh38 versus hg19 (GRCh37), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Somatic mutations from exome and genome sequencing (WXS, WGS), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Genome builds: GRCh38 versus hg19 (GRCh37), Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Variant effect prediction, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Variant effect prediction, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.
Shares Variant effect prediction, Cancer AI vocabulary (CanSim terms map) and the tag cansim-terms.