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how to view points distribution and genes across the whole human genome from a bed position file ?

YingLiuYingLiu ChinaMember
    I have a bed file , then I wanna konw how to view  points  distribution across the whole genome from the  bed  file ,and also mark genes .
    my bed format just like this : chr  start  end  geneName 
    I know IGV can view that ,but  it can export a suitable figure  to inclue the whole genome ,just for every chrosome .



  • shleeshlee ✭✭✭✭✭ CambridgeMember, Broadie ✭✭✭✭✭
    Hi @YingLiu,

    IGV documentation is at
    IGV help is a Google group at!forum/igv-help. I hope you can access it from China.

    You can go to View>Preferences>General and change the _Default Visibility Window_ to `-1`. However, I think your bed data will appear as a histogram in the whole genome view. So I'm not sure how useful that is to you. 
  • YingLiuYingLiu ChinaMember

    @shlee,it's a histogram with loading my bed file . I wanna know whether the bed points distribution is average at the whole genome .

    Issue · Github
    by Sheila

    Issue Number
    Last Updated
    Closed By
  • SheilaSheila admin Broad InstituteMember, Broadie, Moderator admin


    I have asked Soo Hee to get back to you.


  • shleeshlee ✭✭✭✭✭ CambridgeMember, Broadie ✭✭✭✭✭
    edited August 2017

    Hi @YingLiu,

    whether the bed points distribution is average at the whole genome

    Can you clarify further what you need to do?

    1. What you mean by points? Do you mean the score in optional column 5? Or do you mean the across-genome coverage of the bed intervals?

    2. If points/score, do you need to visualize this or quantify the distribution? Or if genomic coverage, are you looking for distribution across the genome?

    If visualization of scores, then I have a vague recollection that bedGraph formats might enable visualization. I'm fuzzy on the details because I've only handled such a file type briefly once. IGV should allow visualization of values either in graph format or there may be a heatmap option. You should ask the IGV help group.

    I'm not sure if this is helpful, but Picard has a tool called IntervalListTools. Note that GATK and Picard use a different index system than BED and so we differentiate by calling our file of genomics intervals intervals_list. In IntervalListTools, there is an option BREAK_BANDS_AT_MULTIPLES_OF that, if it works as I think it does, should enable density calculations in conjunction with another intervals list. If you need something more sophisticated for BED manipulation, then I'm afraid you will have to look elsewhere, perhaps bedtools. Alternatively, try searching the web, SeqAnswers or Biostars to see what solutions other folks have used for your question.

  • shleeshlee ✭✭✭✭✭ CambridgeMember, Broadie ✭✭✭✭✭

    Hi @YingLiu,

    Just to followup from my reply late last night, I think if you are willing to modify your data file to our CNV workflow's seg format, and hack the tool's other requirements (PTN and TN data) then you could use GATK4's PlotSegmentedCopyRatio to view score/point values across the entire genome.

    We explain the CNV workflow at

    This solution is rather circuitous, so I'm sure there are better alternative solutions. It just came to my mind this morning.

  • shleeshlee ✭✭✭✭✭ CambridgeMember, Broadie ✭✭✭✭✭

    I should mention that the last post is just me enumerating possibilities, and the idea is not something our team actually recommends.

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