Question: Problem: GATK insallation
gravatar for chicku
13 months ago by
chicku0 wrote:

Hi I am new to bioinformatics and programming language. I am having trouble installing GATK following the biostar handbook. After install and register, it gives me error message command gatk not found when entered gatk -help. Hoping someone could help me with this.

I downloaded GATK3.8 from and then untar it by tar xjf GATK3.8-1-0-gf15c1c3ef.tar.bz2 then gatk3-register ~/GATK3.8-1-0-gf15c1c3ef/ and then it says it is copying to the environment but I cannot use it....

Please let me know if more information is needed.

gatk • 994 views
ADD COMMENTlink written 13 months ago by chicku0

Please google what PATH is in an Unix environment and how to add executables to it.

ADD REPLYlink written 13 months ago by ATpoint38k

please use GATK4 not 3.8 : . And here is the quick start tutorial from GATK website :

ADD REPLYlink modified 13 months ago • written 13 months ago by Nicolas Rosewick9.0k

alternatively if you are familiar with conda you can install it that way;

ADD REPLYlink written 13 months ago by steve2.6k
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