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  • Seraphya
    Junior Member
    • Oct 2013
    • 4
    #1

    Recommendations for CNV calling algorithms/programs to benchmark

    I want to benchmark the time/resource use and breakpoint accuracy of CNV callers on multiple individual NGS data at 30x-100x coverage at specific CNVs.

    A few questions I have:

    Is there a specific read mapper I should use to create the BAM file, or should I try a few for each SV/CNV caller?

    Are there any specific algorithms/programs I should test? The only one I know I will test for sure is CNVnator as that is what has been used until now.

    Anything else I should consider?
    Tags: cnv annotation, cnv calling, copy number analysis, structrual variation
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