GitHub - egafni/BQSRGatherer_Main: A java class to run GATK BQSRGatherer from the command line

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A java class to run GATK BQSRGatherer from the command line

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Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
BQSRGathererMain.class		BQSRGathererMain.class
BQSRGathererMain.java		BQSRGathererMain.java
README.txt		README.txt
chr20.recal		chr20.recal
log4j.properties		log4j.properties
tiny.recal		tiny.recal

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Compiling
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make sure .jar paths are correct

    javac -classpath ".:Queue-2.4-9-g532efad/Queue.jar:GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.java" BQSRGathererMain.java


Running
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java -cp /home/esg21/WGA/tools/Queue-2.4-9-g532efad/Queue.jar:. BQSRGathererMain test chr20.recal chr21.recal ...