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Question: How to use GATK on Galaxy
1
gravatar for hachemi.zeraia
3.7 years ago by
hachemi.zeraia • 10
United Kingdom
hachemi.zeraia • 10 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 • 2.5k views
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modified 3.7 years ago by Guy Reeves • 1.0k • written 3.7 years ago by hachemi.zeraia • 10

Anyone to help on this

thanks

 

ADD REPLY • link written 3.7 years ago by hachemi.zeraia • 10
1
gravatar for Jennifer Hillman Jackson
3.7 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

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":

http://wiki.galaxyproject.org/Learn#Other_Tutorials

Best, Jen, Galaxy team
ADD COMMENT • link written 3.7 years ago by Jennifer Hillman Jackson ♦ 25k
1
gravatar for Guy Reeves
3.7 years ago by
Guy Reeves • 1.0k
Germany
Guy Reeves • 1.0k wrote:

HI 

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

http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4036707/bin/1756-0500-7-314-S1.pdf

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. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4036707/?tool=pmcentrez

Cheers Guy
ADD COMMENT • link written 3.7 years ago by Guy Reeves • 1.0k
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