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 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

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