Visualizing Data after GATK

[Viberance]

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

[shimbalama]

You'll need to write some custom scripts. Won't take long with Python/Pandas.