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- #!/bin/sh
- #PBS -N mantafusion
- #PBS -j oe
- #PBS -l ncpus=12
- #PBS -l nodes=1
- #PBS -l mem=20G
- #inputpath=$1
- #sample=$2
- source /home/liuxiangqiong/miniconda3/bin/activate python2
- hg19=/cgdata/Database/GATK/b37/human_g1k_v37_decoy.fasta
- outdir=${inputpath}/6Fusion_manta_pair/${tumor}
- mkdir -p ${outdir}
- cd ${inputpath}/6Fusion_manta_pair
- tumorbam=${bam_dir}/${tumor}_clean.bam
- normalbam=${bam_dir}/${normal}_clean.bam
- /cgdata/CGTools/soft/local/bin/python2 /cgdata/xichaowen/Scripts/manta-1.6.0.centos6_x86_64/bin/configManta.py --tumorBam ${tumorbam} --referenceFasta ${hg19} --runDir ${outdir} --exome --normalBam ${normalbam} && /cgdata/CGTools/soft/local/bin/python2 ${outdir}/runWorkflow.py
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