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  • annovar output - question

    I run annovar to annotate my snp file.

    I saw this message:

    WARNING: A total of 273 sequences will be ignored due to lack of correct ORF annotation

    somebody please let me know what's the meaning?

  • #2
    I'm pretty sure that's in reference to sequences it loads from its own databases; nothing to do with your samples. I wouldn't worry about it.

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    • #3
      Thank you

      and futher question...

      the word 'ignored' means that Annovar didn't annotate any gene name and just deleted the SNP??

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      • #4
        I can't remember off the top of my head. Could you copy and paste the text where it says "ignored" (and if it's associated with a specific input line, copy and paste that as well).

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