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gatk-software [2017/02/06 10:50]
joguya created
gatk-software [2018/10/15 16:25] (current)
aorth
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-====== Genome Analysis ToolKit(GATK) ======+====== Genome Analysis ToolKit (GATK) ======
  
 GATK offers a wide variety of tools with a primary focus on variant discovery and genotyping. GATK offers a wide variety of tools with a primary focus on variant discovery and genotyping.
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 ===== Information ===== ===== Information =====
  
-  * Latest Version: ​3.7.0 +  * Latest Version: ​4.0.10.1
-  * Updated: February, 2017+
   * Added: May, 2014   * Added: May, 2014
 +  * Updated: October, 2018
   * Link: https://​software.broadinstitute.org/​gatk/​   * Link: https://​software.broadinstitute.org/​gatk/​
  
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 <​code>​$ module avail gatk</​code>​ <​code>​$ module avail gatk</​code>​
  
-Load gatk +Load one version into your environment and run it: 
-<​code>​$ module load gatk/3.7.0</​code>​+<​code>​$ module load gatk/4.0.10.1 
 +$ gatk</​code>​
  
 ===== Installation ====== ===== Installation ======
- 
 Notes from the sysadmin during installation:​ Notes from the sysadmin during installation:​
-<​code>​ 
-$ cd /tmp 
-$ wget -qO- "​https://​software.broadinstitute.org/​gatk/​download/​auth?​package=GATK"​ | tar xjv 
-$ sudo mkdir /​export/​apps/​gatk/​3.7.0/​ 
-$ sudo chown -R joguya:​joguya /​export/​apps/​gatk/​3.7.0/​ 
-$ sudo cp -rv GenomeAnalysisTK.jar resources/ /​export/​apps/​gatk/​3.7.0/​ 
-</​code>​ 
- 
-I created a generic ''​GenomeAnalysisTK''​ wrapper shell script for GATK, as it must otherwise be run with ''​java -jar ..''​ and is rather user-unfriendly. 
- 
-/​export/​apps/​gatk/​3.7.0/​GenomeAnalysisTK.jar<​code>#​!/​usr/​bin/​env bash 
- 
-readonly PREFIX=$(dirname $0) 
- 
-java -jar $PREFIX/​GenomeAnalysisTK.jar $* 
-</​code>​ 
  
 +<​code>​$ cd /tmp
 +$ wget https://​github.com/​broadinstitute/​gatk/​releases/​download/​4.0.10.1/​gatk-4.0.10.1.zip
 +$ unzip gatk-4.0.10.1.zip
 +$ sudo cp -r gatk-4.0.10.1 /​export/​apps/​gatk/​4.0.10.1</​code>​
gatk-software.1486367444.txt.gz · Last modified: 2017/02/06 10:50 by joguya