# iCNV Integrated copy number variation detection toolset ## Author Zilu Zhou, Nancy R. Zhang ## Maintainer Zilu Zhou <zhouzilu@upenn.edu> Please comment on the *Issues* section for addtional questions. ## Description **iCNV** is a normalization and copy number variation detection procedure for mutiple study designs: WES only, WGS only, SNP array only, or any combination of SNP and sequencing data. **iCNV** applies platform specific normalization, utilizes allele specific reads from sequencing and integrates matched NGS and SNP-array data by a Hidden Markov Model (HMM). ## Installation * Install from GitHub ```r # try http:// if https:// URLs are not supported if (!requireNamespace("BiocManager", quietly=TRUE)) install.packages("BiocManager") BiocManager::install("CODEX") # Install iCNV install.packages("devtools") library(devtools) install_github("zhouzilu/iCNV") ``` ## Update **iCNV** has made a lot of changes on 10/31/2017 for stability, bug fixing and computation power. We strongly recommend you update iCNV to the newest version using the following command. * Update instruction ```r # Remove iCNV remove.packages('iCNV') # reinstall iCNV install.packages("devtools") library(devtools) install_github("zhouzilu/iCNV") ``` ## Workflow overview Number in the parentheses referring to different section in [Vignettes](https://github.com/zhouzilu/iCNV/blob/master/vignettes/iCNV-vignette.Rmd) and function details can be found https://github.com/zhouzilu/iCNV/tree/master/R ``` NGS | Array BAM BED(UCSC for WES or bed_generator.R for WGS 2.2) | SNP Intensity(in standard format) | | | | |----------------| | | | | | |icnv_array_input (2.4) |SAMTools(2.3) |CODEX(2.2) | | | | | |-----------| Variants BAF(vcf) PLR | Array LRR Array BAF | | | | | | | | |SVD(2.4) | | | | | | | | | Normalized LRR | | | | | | ----------------------------------------------------------------------------------- | |iCNV_detection(2.5-2.6) | CNV calling | |icnv_output_to_gb() | Genome Browser input ``` ## Demo code & Vignettes * [Vignettes](https://github.com/zhouzilu/iCNV/blob/master/vignettes/iCNV-vignette.Rmd) * [Vignettes.pdf](https://github.com/zhouzilu/iCNV/blob/master/inst/doc/iCNV-vignette.pdf) * [Vignettes.html](http://htmlpreview.github.io/?https://github.com/zhouzilu/iCNV/blob/master/inst/doc/iCNV-vignette.html) ## Citation Zilu Zhou, Weixin Wang, Li-San Wang, Nancy Ruonan Zhang; Integrative DNA copy number detection and genotyping from sequencing and array-based platforms, Bioinformatics, , bty104, https://doi.org/10.1093/bioinformatics/bty104