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  • Annovar variant filtering

    He guys,
    I m using convert2annovar.pl to convert vcf to avinput , and in this output i have only 14 variants against more then 1000 variants in the input.
    Do you know witch filters apply convert2annovar.pl to reduce the number of variant ?

    Best regards

    Tristan

  • #2
    I don't think there is a filter involved in the conversion, anyways you should get a .log file that tells you all that annovar did on the dataset.

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    • #3
      Thank you for the answer. There is not log file during the conversion (with default mode) i think the log file is create during the annotate_variation.pl

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