A tool for detecting copy number variation (CNV) in various study designs: whole-genome exome sequencing, whole-genome sequencing, and single nucleotide polymorphism (SNP). iCNV (integrated CNV) algorithm the Hidden Markov Model (HMM) to do platform-specific normalization and to integrate sequencing data with SNP-array data.
Exome sequencing; DNA polymorphism; Whole genome sequencing
Zhou Z, Wang W, Wang LS, Zhang NR "Integrative DNA copy number detection and genotyping from sequencing and array-based platforms." Bioinformatics. 2018 Jul 15;34(14):2349-2355. https://doi.org/10.1093/bioinformatics/bty104
PMID: 29992253
PMCID: PMC6041760
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J1, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M "Orchestrating high-throughput genomic analysis with Bioconductor." Nat Methods. 2015 Feb;12(2):115-21. https://doi.org/10.1038/nmeth.3252
PMID: 25633503
PMCID: PMC4509590
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JY, Zhang J. "Bioconductor: open software development for computational biology and bioinformatics." Genome Biol. 2004;5(10):R80. Epub 2004 Sep 15. https://doi.org/10.1186/gb-2004-5-10-r80
PMID: 15461798
PMCID: PMC545600
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