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  • Annovar snp131 rs-number annotation

    Hello all,

    I am testing Annovar, which is a great piece of software. I have encountered a small glitch, however, and were hoping someone else has had the same trouble (and solved it). When annotating with the -geneanno option, I do not get my data annotated with rs-numbers. Therefore, I am trying to get the following command to work:

    Code:
    annotate_variation.pl [B]-dbtype snp131[/B] infile.ann humandb/ -buildver hg19
    In order to do that, I was asked by the program to download the snp131db by issuing the following command:

    Code:
    annotate_variation.pl -downdb snp131 humandb/ -build hg19
    The download and extraction worked fine, but when running the above command, Annovar reports that it doesnt recognize the format:

    Code:
    NOTICE: Reading gene annotation from ../../pipeline/annovar/humandb/hg19_snp131.txt ... Error: invalid record found in ../../pipeline/annovar/humandb/hg19_snp131.txt (chrom field not found): <585     chr1    10433   10433   rs56289060  0+       -       -       -/C     genomic insertion       unknown 0       0       near-gene-5     between 1>
    I find this rather strange, but perhaps anyone else has also seen this?

    Best regards,
    Øyvind

  • #2
    For variant annotation of human genome, would you like to try using VarioWatch to see it fits your needs.


    Adam

    Comment


    • #3
      I guess the -build hg19 is just a typo is it?
      It is supposed to be -buildver hg19
      but if the rest works fine, that can't be the problem.

      Comment


      • #4
        Hi,
        Thats a typo, although I think -build will also work for the downdb-option.

        However, the author of the program kindly pointed out that for snp annotation, I need to use the -filter option, and that solved the issue.

        Comment

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