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  • SNPs distribution plot

    Anyone help me to draw SNPs density of 100kb windows from VCF file.

    Thanks!

  • #2
    Open the VCF file in the latest version of IGV, then zoom out until your desired interval. You can then save the image as PNG or SVG.

    Comment


    • #3
      Try UCSC genome browser. It handles VCF files as a custom track ...

      http://genome.ucsc.edu/cgi-bin/hgCustom (specify your genome and build ). This link may not
      work if you haven't visited the UCSC page before. It needs some cookie variables set first.

      This is the "add custom tracks" button available from the hgTracks page at the UCSC genome browser site.
      Just google "UCSC genome browser " and go browse your favourite genome to set up your UCSC specific cookies.



      Last edited by Richard Finney; 05-14-2015, 05:33 PM.

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      • #4
        Thanks all, but I want to create a plot like the below image...
        Attached Files

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        • #5
          "squish" mode for your custom UCSC track should do that

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