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  • southan
    replied
    You can also use CNVrd2:

    CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.

    Leave a comment:


  • etal
    replied
    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:


  • molcov
    started a topic Inferring absolute copy number by using NGS data

    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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