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java -jar $QUEUE/Queue.jar -noGCOpt -retry 3 -keepIntermediates -statusTo $email -S gatkQueueScript.scala $bams -R $GATKDATA/human_g1k_v37.fasta -D $GATKDATA/dbsnp_138.b37.vcf -genotyper $genotyper -jobRunner Drmaa -jobNative "-t 2:0:0 -n 4 -p short --nodes=1 --mem-per-cpu=8000" 2>&1 | tee $genotyper.log1
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sbatch -q short -t 12:0:0 -mem 8000 --wrap "java -jar $QUEUE/Queue.jar -noGCOpt -retry 3 -keepIntermediates -statusTo $email -S gatkQueueScript.scala $bams -R $GATKDATA/human_g1k_v37.fasta -D $GATKDATA/dbsnp_138.b37.vcf -genotyper $genotyper -jobRunner Drmaa -jobNative \"-t 2:0:0 -n 4 -p short --nodes=1 --mem-per-cpu=8000\" -run 2>&1 | tee $genotyper.log1"
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java -jar $QUEUE/Queue.jar -noGCOpt -retry 3 -keepIntermediates -statusTo $email -S $RCBIO/resource/gatkQueueScript.scala $bams -R $GATKDATA/human_g1k_v37.fasta -D $GATKDATA/dbsnp_138.b37.vcf -genotyper $genotyper -splitNCigarReads -dontUseSoftClippedBases -stand_call_conf 20.0 -jobRunner Drmaa -jobNative "-t 2:0:0 -n 4 -p short --nodes=1 --mem-per-cpu=8000" -startFromScratch
...