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  • Varscan positions output

    Hello everyone,
    I have a quick question and I could not have the answer from the help of varscan.
    I need to know if it is possible to get all the positions of a genome in the output
    of varscan, not only which have snp/indel but everything.
    I tried to change the value of option --variants 1 but it does not change anything.

    Any solution(s) ?

    Thanks in advance,

  • #2
    I've used VarScan2 for a few tests and if I remember correctly the default option (when --variant is not specify) give you all the positions where you've got reads.

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