Question

Visualizing The Outputs Of Gatk/Depthofcoverage

1

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11.3 years ago

Pierre Lindenbaum 161k

Dear lazyweb,

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

P.

gatk depth-of-coverage coverage depth-of-coverage visualization • 6.7k views

ADD COMMENT • link updated 11.3 years ago by Johan ▴ 890 • written 11.3 years ago by Pierre Lindenbaum 161k

0

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

ADD REPLY • link 7.5 years ago by Jeremy Leipzig 22k

score 5 · Accepted Answer · 2013-01-18

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.