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  • Viberance
    Member
    • Feb 2015
    • 13
    #1

    Visualizing Data after GATK

    Hi I have about 80 samples. I ran GATK on it to do DepthofCoverage and generated all the following files


    Coverage_summary
    Coverage_summary.sample_cumulative_coverage_counts
    Coverage_summary.sample_cumulative_coverage_proportions
    Coverage_summary.sample_interval_statistics
    Coverage_summary.sample_interval_summary
    Coverage_summary.sample_statistics
    Coverage_summary.sample_summary
    I want to create a table with all samples showing Sample ID, targeted regions, depth for forward read, Depth for reverse read, Median Depth for that target


    And then I want to be able to plot this data showing per sample median depth per targeted region.


    Any suggestion is appreciated


    Thank you
    Tags: None
  • shimbalama
    bioinformatics-help.com
    • Jul 2014
    • 9
    #2
    You'll need to write some custom scripts. Won't take long with Python/Pandas.
    LM

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