Question: How to use GATK on Galaxy
gravatar for hachemi.zeraia
2.9 years ago by
United Kingdom
hachemi.zeraia0 wrote:

Dear All

Could we get directed or shown an example how one can use GATK on Galaxy ( simple data example) step by step

i am bit stuck


help gatk • 1.8k views
ADD COMMENTlink modified 2.8 years ago by Guy Reeves1.0k • written 2.9 years ago by hachemi.zeraia0

Anyone to help on this



ADD REPLYlink written 2.8 years ago by hachemi.zeraia0
gravatar for Jennifer Hillman Jackson
2.8 years ago by
United States
Jennifer Hillman Jackson23k wrote:


The tutorial from the Davis group is a good place to start. It is linked from our wiki here, under "UC Davis 2013 Bioinformatics Short Course":

Best, Jen, Galaxy team

ADD COMMENTlink written 2.8 years ago by Jennifer Hillman Jackson23k
gravatar for Guy Reeves
2.8 years ago by
Guy Reeves1.0k
Guy Reeves1.0k wrote:


I sure that the link that Jen gave you above is very good, personally I found this .pdf to be very useful in explaining what to do and why on GATK

If you ignore the cloud context it gives you a good idea what to do even if you do not work with human data.  It is actually a supplementary file to the following paper.

Cheers Guy

ADD COMMENTlink written 2.8 years ago by Guy Reeves1.0k
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