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  • Some problem in the output of CNVnator

    why I type
    ./cnvnator -root out1.root -view 100
    >

    just appears a ">" on the screen, out1.root is for chrom 1.

    This problem happens when I use -genotype
    ./cnvnator -root out1.root -genotype 100
    >

    Anyone can give me some advise?Thx!

  • #2
    Hello,
    This is from the CNVnator manual.

    ********
    >>>VISUALIZING SPECIFIED REGIONS

    ./cnvnator -root file.root [-chrom chr_name1 ...] -view bin_size [-ngc]

    Once prompted enter a genomic region, e.g.
    >chr12:11396601-11436500
    or
    >chr12 11396601 11436500

    Additionally one can specify length of flanking regions (default is 10 kb) to
    be also displayed, e.g.
    >chr12:11396601-11436500 100000
    or
    >chr12 11396601 11436500 100000

    One can also perform instant genotyping by adding word 'genotype', e.g.
    >chr12:11396601-11436500 genotype
    or
    >chr12 11396601 11436500 genotype

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