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manta_script.sh
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mkdir /work/manta
mkdir /work/manta/III20
mkdir /work/manta/III21
mkdir /work/manta/IV33
mkdir /work/manta/V14
configManta.py --bam /work/my_data/III20_proc/III20.sorted.deduplicated.recalibrated.bam --referenceFasta /work/reference/hg38/Homo_sapiens_assembly38.fasta --runDir /work/manta/III20
configManta.py --bam /work/my_data/III21_proc/III21.sorted.deduplicated.recalibrated.bam --referenceFasta /work/reference/hg38/Homo_sapiens_assembly38.fasta --runDir /work/manta/III21
configManta.py --bam /work/my_data/IV33_proc/IV33.sorted.deduplicated.recalibrated.bam --referenceFasta /work/reference/hg38/Homo_sapiens_assembly38.fasta --runDir /work/manta/IV33
configManta.py --bam /work/my_data/V14_proc/V14.sorted.deduplicated.recalibrated.bam --referenceFasta /work/reference/hg38/Homo_sapiens_assembly38.fasta --runDir /work/manta/V14
python /work/manta/III20/runWorkflow.py -m local
python /work/manta/III21/runWorkflow.py -m local
python /work/manta/IV33/runWorkflow.py -m local
python /work/manta/V14/runWorkflow.py -m local