I have genomic positions in a tab delimited file as follows:

    Chr     Start   End
    2       10262865        11801950
    2       9637403          10927601
    2       25141434        27157396
    2       31181368        38044662
    2       127808684       129276101
    2       236957807       238896574
    2       237172736       238896574

 
**First I want to find overlapping segments within these genomic segments in the same file (edit)**. Then I wish to plot these such that the segments do not overlap on the plot.  Is there a tool that can aid in::
1 Finding overlapping regions within the same file
2. Visualising the segments in a non-overlapping manner? 

My attempts at plotting this in R results in the segments occupying the same position

If you want to plot them, you can use [karyoploteR](http://bioconductor.org/packages/karyoploteR/). The function [kpPlotRegions](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotRegions/PlotRegions.html) plot the regions non-overlapping by default and will create the plot I think you asking for. 

The first two lines read the data file into a GenomicRanges object and change the chromosome names to the ones used by the default genome (UCSC hg19). [plotKaryotype](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/CreateIdeogram/CreateIdeogram.html) creates the plot and [kpPlotRegions](https://bernatgel.github.io/karyoploter_tutorial//Tutorial/PlotRegions/PlotRegions.html) adds the region to the plot. At the [karyoploteR tutorial](https://bernatgel.github.io/karyoploter_tutorial/) you can find more information on how to add more data and customize your plots.

    library(karyoploteR)

    regions <- toGRanges("regions.txt")
    seqlevelsStyle(regions) <- "UCSC"

    kp <- plotKaryotype(chromosomes="chr2")
    kpPlotRegions(kp, data=regions)

![enter image description here][1]

  [1]: https://raw.githubusercontent.com/bernatgel/karyoploteR_questions/master/biostars_367522/plot.png