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  • Annovar annotation with 1000g

    Hello everyone,

    I have recently downloaded Annovar, and succesfully filtered my files with a few databases, downloaded from Annovar.
    But when I try to do the exact same thing with the 1000 genomes project database, I get this error many times in the terminal, one for each line of **.

    Argument "*" isn't numeric in numeric eq (==) at annotate_variation.pl line 1962, <DB> line **.
    * can be A, C, G, or T.
    ** every line of the database

    I have tried filtering with 1000g, 1000g2010 and 1000g2010jul databases, but all give these errors.

    An example of the commands I use for filtering:
    perl annotate_variation.pl --filter --dbtype CEU.sites.2010_07 testfile1.txt humandb/

    Can anyone tell me if I'm doing something wrong, if this is known, and if I can do anything about it?

  • #2
    Originally posted by Jamica View Post
    Hello everyone,

    I have recently downloaded Annovar, and succesfully filtered my files with a few databases, downloaded from Annovar.
    But when I try to do the exact same thing with the 1000 genomes project database, I get this error many times in the terminal, one for each line of **.

    Argument "*" isn't numeric in numeric eq (==) at annotate_variation.pl line 1962, <DB> line **.
    * can be A, C, G, or T.
    ** every line of the database

    I have tried filtering with 1000g, 1000g2010 and 1000g2010jul databases, but all give these errors.

    An example of the commands I use for filtering:
    perl annotate_variation.pl --filter --dbtype CEU.sites.2010_07 testfile1.txt humandb/

    Can anyone tell me if I'm doing something wrong, if this is known, and if I can do anything about it?

    Have you fixed your problem? How?

    I get the same error with the latest 1000g dataset, 1000g2015aug.zip which extracts 6 .txt files:
    hg19_ALL.sites.2015_08.txt
    hg19_AFR.sites.2015_08.txt
    hg19_AMR.sites.2015_08.txt
    hg19_EUR.sites.2015_08.txt
    hg19_SAS.sites.2015_08.txt
    hg19_EAS.sites.2015_08.txt

    while running the command:
    Code:
    perl table_annovar.pl tumor-vs-normal.mutect.vcf humandb/ -outfile temp/myanno -protocol ALL.sites.2015_08 -operation f -nastring . -vcfinput -remove -thread 12
    Last edited by arkanion; 09-15-2016, 10:14 PM. Reason: corrected command

    Comment


    • #3
      Try using '-protocol 1000g2015aug_all' in your command, and let us know if that solves your problem or not.

      Comment

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