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GATK-Script

./install.sh will install ~/local/bin/GATK.py along with necessary *.jar files in ~/local/share/gatk and ~/local/share/picard_tools/.

Make sure $PATH includes ~/local/bin and run the command GATK.py -r <input.gbk> <read1.fastq read2.fastq ...> to create an output.vcf file.

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