Discovery of copy number variations (CNVs) from exome read depth using XHMM (eXome-Hidden Markov Model)

Call copy number variation (CNV) from next-generation sequencing data, where exome capture was used (or targeted sequencing, more generally).

Input files:

1. list of exome targets ("EXOME.interval_list", one column format of exome regions of one specific chromosome, e.g., 10:92895-94177)
2. exome sequencing reads ("DATA.RD.txt", matrix of all coverage means for all EXOME.interval_list regions of all samples, obtained from GATK pipeline)
3. Markov model parameters ("params.txt", all 9 model parameters)

Please see the following link for original source code: http://atgu.mgh.harvard.edu/xhmm/download.shtml

Installing/using the XHMM R scripts

The XHMM R code is now available as an R library. There are still two options for using the scripts:

Newer (preferred) option

Install the xhmmScripts package via one of the following methods (you only need to do this once):

1. Compile it from the main XHMM source code downloaded from the Git repository above: cd statgen-xhmm-* make R Then, run in R: install.packages(list.files(path=".", pattern="xhmmScripts_.+\.tar\.gz"), repos=NULL, type="source")

2. Download and install the package from CRAN using the install.packages() command in R: install.packages("xhmmScripts")

3. Download it from the xhmmScripts page at CRAN. Then, run in R: install.packages(list.files(path=".", pattern="xhmmScripts_.+\.tar\.gz"), repos=NULL, type="source")

To use the R code, preface your R scripts with: library(xhmmScripts)