Inferring absolute copy number by using NGS data

[molcov]

Hi all,

I have a set of CNV loci called from NGS data, and now I want to do genotyping, i.e. inferring the absolute copy number from this dataset. To my knowledge CopySeq can do this work, but unfortunately I cannot run CopySeq successfully. Does anyone know how to run CopySeq or is there any other read-depth-based software that can do the same work?

Thanks in advance..

[etal]

THetA2 can infer absolute copy number from read depth: http://compbio.cs.brown.edu/projects/theta/

It runs using the segmentation output of BIC-seq, ExomeCNV, EXCAVATOR or CNVkit, and infers the tumor cell purity, subclone composition if present, and absolute copy number of each segment.

[southan]

You can also use CNVrd2:

http://www.bioconductor.org/packages/devel/bioc/html/CNVrd2.html