You can also use CNVrd2:
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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.Leave a comment:
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Inferring absolute copy number by using NGS data
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..
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