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GenomeAnalysisTK.jar and Picard.jar were separate tools up to GATK v3.8. But from v4, Picard has been integrated into the Genome Analysis toolkit. You are not reading the most recent version of this documentation. v1.3.2 is the gatk ==3.8 optional threads: 16 wrapper: "bio/gatk/indelrealigner". bioconda / packages / gatk 3.8. 3. The full Genome Analysis Toolkit (GATK) framework, license restricted. conda install -c bioconda gatk License. The versions of GATK in this repository are licensed by the Broad Institute and are made available for free to academic users for non-commercial usejava -jar /software/gatk/3.8/static/GenomeAnalysisTK.jar -T RealignerTargetCreator -h. You should try looking at the help documentation for each of the GATK