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task manta_calling{ |
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task manta_calling{ |
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File tumour_bam |
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File tumour_bam_bai |
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File tumor_bam |
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File tumor_bam_bai |
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File normal_bam |
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File normal_bam |
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File normal_bam_bai |
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File normal_bam_bai |
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String ref_fasta |
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String ref_fasta |
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nt=$(nproc) |
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nt=$(nproc) |
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/home/biosoft/manta-1.6.0.centos6_x86_64/bin/configManta.py \ |
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/home/biosoft/manta-1.6.0.centos6_x86_64/bin/configManta.py \ |
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--normalBam ${normal_bam} \ |
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--normalBam ${normal_bam} \ |
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--tumorBam ${tumour_bam} \ |
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--tumorBam ${tumor_bam} \ |
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--referenceFasta ${ref_dir}/${ref_fasta} \ |
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--referenceFasta ${ref_dir}/${ref_fasta} \ |
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--runDir ${out_dir} |
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--runDir ${out_dir} |
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