gatk-software
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gatk-software [2017/02/06 07:50] – created joguya | gatk-software [2023/05/11 09:59] (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. | ||
Line 5: | Line 5: | ||
===== Information ===== | ===== Information ===== | ||
- | * Latest Version: | + | * Latest Version: |
- | * Updated: February, 2017 | + | |
* Added: May, 2014 | * Added: May, 2014 | ||
- | * Link: https://software.broadinstitute.org/gatk/ | + | |
+ | | ||
===== Usage ===== | ===== Usage ===== | ||
- | See which versions | + | See which versions are available: |
< | < | ||
- | Load gatk | + | Load one version into your environment and run it: |
- | < | + | < |
+ | $ gatk</ | ||
+ | |||
+ | **Note:** The HaplotypeCaller step can scale to multiple CPUs/ | ||
===== Installation ====== | ===== Installation ====== | ||
- | |||
Notes from the sysadmin during installation: | Notes from the sysadmin during installation: | ||
- | < | ||
- | $ cd /tmp | ||
- | $ wget -qO- " | ||
- | $ sudo mkdir / | ||
- | $ sudo chown -R joguya: | ||
- | $ sudo cp -rv GenomeAnalysisTK.jar resources/ / | ||
- | </ | ||
- | |||
- | I created a generic '' | ||
- | |||
- | / | ||
- | |||
- | readonly PREFIX=$(dirname $0) | ||
- | java -jar $PREFIX/GenomeAnalysisTK.jar $* | + | < |
- | </ | + | $ wget https:// |
+ | $ unzip gatk-4.4.0.0.zip | ||
+ | $ sed -i ' | ||
+ | $ sudo cp -r gatk-4.4.0.0 / | ||
+ | **Note (2023-05-11): |
gatk-software.1486367444.txt.gz · Last modified: 2017/02/06 07:50 by joguya