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  • Annovar

    How can I add additional annotations like the gwas db or omim db to the output of summarize_annovar.pl either as an option for that script or after the output is already generated? Either way, I want these databases added to my annotated variant list from the summarize_annovar.pl script.

    Any help would be much appreciated.

    Thanks,

    Nathan

  • #2
    I try and it work fine before with the following command:
    eg
    Code:
    perl annotate_variation.pl -downdb -buildver hg19 hg19_phastConsElements46way.txt humandb/
    I download one by one last time.
    However I notice I can't access annovar website since this morning
    Can you still access annovar website?

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    • #3
      Thanks, I used that script to download the databases. I just need to figure out how to put all those databases together.

      The annovar website seems to be down right now. I just tried and it was unable to connect.

      Comment


      • #4
        Hi Cable,

        Do you have the email address regarding help support of annovar website?
        I plan to ask why can't access it since this morning
        You just need to download all the database and save inside humandb.
        I guess it should be able to work fiine...
        Maybe you can explain more about your problem.
        I will try to share with you if I know

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        • #5
          not to change the topic but snpEFF works quite awesome too

          Comment


          • #6
            I have heard about snpEFF...I think I will try that one out too...thanks.

            Edge: I cannot recall the email for Annovar supprt. As far as downloading, I did download all the databases into my humandb folder and annotated using the summarize_annovar script. There are additional databases I want to add to the output file of summarize_annovar and that is what I was asking about.

            Comment


            • #7
              Annovar support email

              The annovar support email (according to my cached version of the annovar page):

              [email protected]

              Comment


              • #8
                Originally posted by adaptivegenome View Post
                not to change the topic but snpEFF works quite awesome too
                Annovar is more powerfull than SNPeff and Seattleseq.

                Comment


                • #9
                  Originally posted by Cable View Post
                  How can I add additional annotations like the gwas db or omim db to the output of summarize_annovar.pl either as an option for that script or after the output is already generated? Either way, I want these databases added to my annotated variant list from the summarize_annovar.pl script.

                  Any help would be much appreciated.

                  Thanks,

                  Nathan
                  After annotating your data by summarize-annovar.pl which would generate several temporal files and one file with all the annotations -(which is probablely called Genome...)- if you want to add more data to it, move the chr, strat, end, ref., alter. columns to the 1st,2,3,4 and 5th columns respectively and run this command:
                  perl annotate_variation.pl -filter -dbtype <omim/any-database> <your-file> humandb/
                  Last edited by Rez; 10-24-2012, 12:49 PM.

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