Visualizing The Outputs Of Gatk/Depthofcoverage

Question

[Pierre Lindenbaum]

Dear lazyweb,

do you know any tool/script to visualize the different outputs of GATK DepthOfCoverage ?

P.

[Jeremy Leipzig]

weird there are not more options for this as common as gatk is

Answer 1

[Johan]

I wrote these scripts some time ago:

https://github.com/johandahlberg/Scripts/blob/master/plottingLociVsCoverage.R

https://github.com/johandahlberg/Scripts/blob/master/plottingCumulativeCoverage.R

R really isn't my strong suite, but at least its something, and they served my purpose at the time. I would be happy to accept any pull requests to improve on them, though.