Vertaile menetelmiä

	Differentiaalinen varianttien kutsuminen	Kopiolukuvaihtelun analyysi – CNV:n havaitseminen ja tulkinta
Tieteenala	Bioinformatiikka	Bioinformatiikka
Menetelmäperhe	Process / pipeline	Process / pipeline
Syntyvuosi	2009–2013 (field matured with NGS; seminal tools 2009–2013)	1998–2006
Kehittäjä	Multiple groups; key tools: VarScan (Koboldt et al.), MuTect (Cibulskis et al.), GATK Haplotype Caller (DePristo et al.)	Pinkel et al. (array CGH); Redon et al. (genome-wide CNV map)
Tyyppi	Comparative genomic analysis pipeline	Genomic structural variant detection pipeline
Alkuperäislähde	Koboldt, D.C., Zhang, Q., Larson, D.E., Shen, D., McLellan, M.D., Lin, L., Miller, C.A., Mardis, E.R., Ding, L., & Wilson, R.K. (2012). VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing. Genome Research, 22(3), 568–576.	Redon, R., Ishikawa, S., Fitch, K. R., et al. (2006). Global variation in copy number in the human genome. Nature, 444(7118), 444–454.
Rinnakkaisnimet	somatic variant calling, comparative variant analysis, tumor-normal variant calling, differential SNV/indel calling	CNV analysis, copy number variant detection, CNV calling, somatic copy number alteration analysis
Liittyvät	2	6
Tiivistelmä	Differential variant calling is a bioinformatics pipeline that identifies genetic variants — single nucleotide variants (SNVs), small insertions/deletions (indels), and structural variants — that are present in one biological sample or condition but absent (or significantly enriched) in a paired reference sample. The canonical application is tumor-versus-normal cancer genomics, where somatic mutations unique to the tumor are distinguished from germline variants shared with normal tissue. The same logic applies to comparing treated vs. untreated cell lines, evolved vs. ancestral strains, or case vs. control cohorts in population genomics.	Copy number variation (CNV) analysis is a genomic pipeline for detecting regions where individuals carry fewer or more copies of a DNA segment than the reference genome. CNVs span kilobases to megabases and are a major class of structural variation implicated in cancer, neurodevelopmental disorders, and population diversity. The pipeline typically processes SNP array intensities or read-depth signals from whole-genome sequencing, applies segmentation algorithms, calls gain and loss events, and annotates them against gene and clinical databases.