runbsub -n 1 -q brc -W 7000 -o std.out -e std.err -N __bsubArgsEnd__ runner cp /gpfs_common/mobyle_share/data/None ref.fasta % java -Xmx16g -Djava.io.tmpdir=tmp -jar /home/mobyle/bin/picard-tools-1.88/CreateSequenceDictionary.jar TMP_DIR=tmp R=ref.fasta O=ref.dict % python /home/mobyle/bin/merge_vcf.py /usr/local/apps/java/jre1.6.0_31/bin/java -jar /home/mobyle/bin/GenomeAnalysisTK-2.4-9-g532efad/GenomeAnalysisTK.jar -T CombineVariants -R ref.fasta -o merged.vcf -genotypeMergeOptions UNSORTED