This is a method for Allele-specific DNA Copy Number profiling for whole-Exome sequencing data. Given the allele-specific coverage and site biases at the variant loci, this program segments the genome into regions of homogeneous allele-specific copy number. It requires, as input, the read counts for each variant allele in a pair of case and control samples, as well as the site biases. For detection of somatic mutations, the case and control samples can be the tumor and normal sample from the same individual. The implemented method is based on the paper: Chen, H., Jiang, Y., Maxwell, K., Nathanson, K. and Zhang, N. (under review). Allele-specific copy number estimation by whole Exome sequencing.
|Author||Hao Chen and Nancy R. Zhang|
|Date of publication||2017-02-24 23:43:44|
|Maintainer||Hao Chen <email@example.com>|
|License||GPL (>= 2)|
biasMatrix: Bias Matrix
falconx: Finding Allele-Specific Copy Number in Whole-Exome Sequencing...
getASCN.x: Getting Allele-specific DNA Copy Number
getChangepoints.x: Getting Change-points
pos: Position (bp)
readMatrix: Reads Matrix
tauhat: Estimated Break Points
view: Viewing Data with Allele-specific Copy Number