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  • bair
    Member
    • Jan 2010
    • 65

    #1

    Compare SNPs

    Hello, does someone know how to comare two SNP calling files in gff format?

    Thanks for your help!
  • quinlana
    Senior Member
    • Sep 2008
    • 119

    #2
    I would suggest Galaxy if you want a web interface or BEDTools if you prefer command line tools.

    Aaron
    Disclosure: I am the author of BEDTools.

    Comment

    • bair
      Member
      • Jan 2010
      • 65

      #3
      That's exactly what I am looking, very useful.

      Thanks

      Comment

      • bair
        Member
        • Jan 2010
        • 65

        #4
        installed BEDtools (BEDTools.v2.4.2.tar.gz), but only has bamToBed under bin/

        other tools?

        Comment

        • quinlana
          Senior Member
          • Sep 2008
          • 119

          #5
          That's quite odd.

          Did you type "make" then Enter in the BEDTools directory? This should have compiled all 17 tools and placed the resulting binaries in bin/

          Comment

          • bair
            Member
            • Jan 2010
            • 65

            #6
            Hi Quinlana,

            Got all 17 tools with the help from our admin. BTW, when I only type bedtools, all the 17 tools should be list, otherwise I have to go to the path to find out which function bedtools has.

            Thanks

            Comment

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